Mercurial > repos > eschen42 > mqppep_anova

annotate mqppep_mrgfltr.py @ 11:254ab97c6a2c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 681875e344ae25ccd421df12da01bc5521a6a7c7"
author eschen42
date Tue, 15 Mar 2022 12:44:40 +0000
parents 922d309640db
children
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d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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1 #!/usr/bin/env python
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2
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3 # Import the packages needed
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4 import argparse
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5 import operator # for operator.itemgetter
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6 import os.path
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7 import re
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8 import shutil # for shutil.copyfile(src, dest)
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9 import sqlite3 as sql
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10 import sys # import the sys module for exc_info
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11 import time
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12 import traceback # for formatting stack-trace
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13 from codecs import getreader as cx_getreader
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d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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15 import numpy as np
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16 import pandas
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18 # global constants
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19 N_A = "N/A"
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22 # ref: https://stackoverflow.com/a/8915613/15509512
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23 # answers: "How to handle exceptions in a list comprehensions"
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24 # usage:
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25 # from math import log
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26 # eggs = [1,3,0,3,2]
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27 # print([x for x in [catch(log, egg) for egg in eggs] if x is not None])
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28 # producing:
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29 # for <built-in function log>
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30 # with args (0,)
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31 # exception: math domain error
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32 # [0.0, 1.0986122886681098, 1.0986122886681098, 0.6931471805599453]
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33 def catch(func, *args, handle=lambda e: e, **kwargs):
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34
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35 try:
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36 return func(*args, **kwargs)
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37 except Exception as e:
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38 print("For %s" % str(func))
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39 print(" with args %s" % str(args))
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40 print(" caught exception: %s" % str(e))
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41 (ty, va, tb) = sys.exc_info()
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42 print(" stack trace: " + str(traceback.format_exception(ty, va, tb)))
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43 exit(-1)
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44 return None
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45
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46
6
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47 def whine(func, *args, handle=lambda e: e, **kwargs):
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48
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49 try:
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50 return func(*args, **kwargs)
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51 except Exception as e:
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52 print("Warning: For %s" % str(func))
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53 print(" with args %s" % str(args))
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54 print(" caught exception: %s" % str(e))
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55 (ty, va, tb) = sys.exc_info()
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56 print(" stack trace: " + str(traceback.format_exception(ty, va, tb)))
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57 return None
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58
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59
5
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60 def ppep_join(x):
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61 x = [i for i in x if N_A != i]
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62 result = "%s" % " | ".join(x)
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63 if result != "":
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64 return result
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65 else:
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66 return N_A
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67
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68
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69 def melt_join(x):
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70 tmp = {key.lower(): key for key in x}
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71 result = "%s" % " | ".join([tmp[key] for key in tmp])
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72 return result
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73
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74
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75 def __main__():
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76 # Parse Command Line
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77 parser = argparse.ArgumentParser(
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78 description="Phopsphoproteomic Enrichment Pipeline Merge and Filter."
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79 )
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80
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81 # inputs:
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82 # Phosphopeptide data for experimental results, including the intensities
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83 # and the mapping to kinase domains, in tabular format.
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84 parser.add_argument(
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85 "--phosphopeptides",
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86 "-p",
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87 nargs=1,
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88 required=True,
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89 dest="phosphopeptides",
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90 help="Phosphopeptide data for experimental results, including the intensities and the mapping to kinase domains, in tabular format",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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91 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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92 # UniProtKB/SwissProt DB input, SQLite
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93 parser.add_argument(
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94 "--ppep_mapping_db",
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95 "-d",
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96 nargs=1,
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97 required=True,
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98 dest="ppep_mapping_db",
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99 help="UniProtKB/SwissProt SQLite Database",
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100 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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101 # species to limit records chosed from PhosPhositesPlus
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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102 parser.add_argument(
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103 "--species",
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104 "-x",
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105 nargs=1,
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106 required=False,
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107 default=[],
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108 dest="species",
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109 help="limit PhosphoSitePlus records to indicated species (field may be empty)",
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110 )
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111
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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112 # outputs:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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113 # tabular output
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114 parser.add_argument(
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115 "--mrgfltr_tab",
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116 "-o",
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117 nargs=1,
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118 required=True,
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119 dest="mrgfltr_tab",
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120 help="Tabular output file for results",
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121 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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122 # CSV output
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123 parser.add_argument(
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124 "--mrgfltr_csv",
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125 "-c",
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126 nargs=1,
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127 required=True,
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128 dest="mrgfltr_csv",
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129 help="CSV output file for results",
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130 )
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131 # SQLite output
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132 parser.add_argument(
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133 "--mrgfltr_sqlite",
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134 "-S",
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135 nargs=1,
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136 required=True,
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137 dest="mrgfltr_sqlite",
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138 help="SQLite output file for results",
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139 )
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140
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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141 # "Make it so!" (parse the arguments)
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142 options = parser.parse_args()
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143 print("options: " + str(options))
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144
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145 # determine phosphopeptide ("upstream map") input tabular file access
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146 if options.phosphopeptides is None:
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147 exit('Argument "phosphopeptides" is required but not supplied')
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148 try:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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149 upstream_map_filename_tab = os.path.abspath(options.phosphopeptides[0])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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150 input_file = open(upstream_map_filename_tab, "r")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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151 input_file.close()
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152 except Exception as e:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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153 exit("Error parsing phosphopeptides argument: %s" % str(e))
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154
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155 # determine input SQLite access
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156 if options.ppep_mapping_db is None:
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157 exit('Argument "ppep_mapping_db" is required but not supplied')
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158 try:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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159 uniprot_sqlite = os.path.abspath(options.ppep_mapping_db[0])
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160 input_file = open(uniprot_sqlite, "rb")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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161 input_file.close()
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162 except Exception as e:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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163 exit("Error parsing ppep_mapping_db argument: %s" % str(e))
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164
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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165 # copy input SQLite dataset to output SQLite dataset
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166 if options.mrgfltr_sqlite is None:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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167 exit('Argument "mrgfltr_sqlite" is required but not supplied')
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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168 try:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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169 output_sqlite = os.path.abspath(options.mrgfltr_sqlite[0])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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170 shutil.copyfile(uniprot_sqlite, output_sqlite)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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171 except Exception as e:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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172 exit("Error copying ppep_mapping_db to mrgfltr_sqlite: %s" % str(e))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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173
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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174 # determine species to limit records from PSP_Regulatory_Sites
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175 if options.species is None:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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176 exit(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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177 'Argument "species" is required (and may be empty) but not supplied'
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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178 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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179 try:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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180 if len(options.species) > 0:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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181 species = options.species[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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182 else:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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183 species = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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184 except Exception as e:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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185 exit("Error parsing species argument: %s" % str(e))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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186
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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187 # determine tabular output destination
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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188 if options.mrgfltr_tab is None:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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189 exit('Argument "mrgfltr_tab" is required but not supplied')
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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190 try:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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191 output_filename_tab = os.path.abspath(options.mrgfltr_tab[0])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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192 output_file = open(output_filename_tab, "w")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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193 output_file.close()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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194 except Exception as e:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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195 exit("Error parsing mrgfltr_tab argument: %s" % str(e))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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196
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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197 # determine CSV output destination
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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198 if options.mrgfltr_csv is None:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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199 exit('Argument "mrgfltr_csv" is required but not supplied')
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
200 try:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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201 output_filename_csv = os.path.abspath(options.mrgfltr_csv[0])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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202 output_file = open(output_filename_csv, "w")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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203 output_file.close()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
204 except Exception as e:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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205 exit("Error parsing mrgfltr_csv argument: %s" % str(e))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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206
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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207 def mqpep_getswissprot():
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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208
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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209 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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210 # copied from Excel Output Script.ipynb BEGIN #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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211 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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212
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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213 # String Constants #################
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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214 DEPHOSPHOPEP = "DephosphoPep"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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215 DESCRIPTION = "Description"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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216 FUNCTION_PHOSPHORESIDUE = (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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217 "Function Phosphoresidue(PSP=PhosphoSitePlus.org)"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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218 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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219 GENE_NAME = "Gene_Name" # Gene Name from UniProtKB
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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220 ON_FUNCTION = (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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221 "ON_FUNCTION" # ON_FUNCTION column from PSP_Regulatory_Sites
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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222 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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223 ON_NOTES = "NOTES" # NOTES column from PSP_Regulatory_Sites
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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224 ON_OTHER_INTERACT = "ON_OTHER_INTERACT" # ON_OTHER_INTERACT column from PSP_Regulatory_Sites
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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225 ON_PROCESS = (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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226 "ON_PROCESS" # ON_PROCESS column from PSP_Regulatory_Sites
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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227 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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228 ON_PROT_INTERACT = "ON_PROT_INTERACT" # ON_PROT_INTERACT column from PSP_Regulatory_Sites
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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229 PHOSPHOPEPTIDE = "Phosphopeptide"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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230 PHOSPHOPEPTIDE_MATCH = "Phosphopeptide_match"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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231 PHOSPHORESIDUE = "Phosphoresidue"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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232 PUTATIVE_UPSTREAM_DOMAINS = "Putative Upstream Kinases(PSP=PhosphoSitePlus.org)/Phosphatases/Binding Domains"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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233 SEQUENCE = "Sequence"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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234 SEQUENCE10 = "Sequence10"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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235 SEQUENCE7 = "Sequence7"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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236 SITE_PLUSMINUS_7AA_SQL = "SITE_PLUSMINUS_7AA"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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237 UNIPROT_ID = "UniProt_ID"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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238 UNIPROT_SEQ_AND_META_SQL = """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
239 select Uniprot_ID, Description, Gene_Name, Sequence,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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240 Organism_Name, Organism_ID, PE, SV
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
241 from UniProtKB
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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242 order by Sequence, UniProt_ID
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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243 """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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244 UNIPROT_UNIQUE_SEQ_SQL = """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
245 select distinct Sequence
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
246 from UniProtKB
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
247 group by Sequence
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
248 """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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249 PPEP_PEP_UNIPROTSEQ_SQL = """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
250 select distinct phosphopeptide, peptide, sequence
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
251 from uniprotkb_pep_ppep_view
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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252 order by sequence
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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253 """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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254 PPEP_MELT_SQL = """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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255 SELECT DISTINCT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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256 phospho_peptide AS 'p_peptide',
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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257 kinase_map AS 'characterization',
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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258 'X' AS 'X'
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
259 FROM ppep_gene_site_view
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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260 """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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261 # CREATE TABLE PSP_Regulatory_site (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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262 # site_plusminus_7AA TEXT PRIMARY KEY ON CONFLICT IGNORE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
263 # domain TEXT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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264 # ON_FUNCTION TEXT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
265 # ON_PROCESS TEXT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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266 # ON_PROT_INTERACT TEXT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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267 # ON_OTHER_INTERACT TEXT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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268 # notes TEXT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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269 # organism TEXT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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270 # );
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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271 PSP_REGSITE_SQL = """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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272 SELECT DISTINCT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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273 SITE_PLUSMINUS_7AA ,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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274 DOMAIN ,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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275 ON_FUNCTION ,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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276 ON_PROCESS ,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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277 ON_PROT_INTERACT ,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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278 ON_OTHER_INTERACT ,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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279 NOTES ,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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280 ORGANISM
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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281 FROM PSP_Regulatory_site
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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282 """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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283 PPEP_ID_SQL = """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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284 SELECT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
285 id AS 'ppep_id',
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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286 seq AS 'ppep_seq'
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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287 FROM ppep
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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288 """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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289 MRGFLTR_DDL = """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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290 DROP VIEW IF EXISTS mrgfltr_metadata_view;
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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291 DROP TABLE IF EXISTS mrgfltr_metadata;
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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292 CREATE TABLE mrgfltr_metadata
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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293 ( ppep_id INTEGER REFERENCES ppep(id)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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294 , Sequence10 TEXT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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295 , Sequence7 TEXT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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296 , GeneName TEXT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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297 , Phosphoresidue TEXT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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298 , UniProtID TEXT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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299 , Description TEXT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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300 , FunctionPhosphoresidue TEXT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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301 , PutativeUpstreamDomains TEXT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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302 , PRIMARY KEY (ppep_id) ON CONFLICT IGNORE
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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303 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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304 ;
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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305 CREATE VIEW mrgfltr_metadata_view AS
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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306 SELECT DISTINCT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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307 ppep.seq AS phospho_peptide
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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308 , Sequence10
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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309 , Sequence7
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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310 , GeneName
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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311 , Phosphoresidue
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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312 , UniProtID
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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313 , Description
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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314 , FunctionPhosphoresidue
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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315 , PutativeUpstreamDomains
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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316 FROM
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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317 ppep, mrgfltr_metadata
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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318 WHERE
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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319 mrgfltr_metadata.ppep_id = ppep.id
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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320 ORDER BY
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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321 ppep.seq
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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322 ;
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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323 """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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324
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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325 CITATION_INSERT_STMT = """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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326 INSERT INTO Citation (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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327 ObjectName,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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328 CitationData
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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329 ) VALUES (?,?)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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330 """
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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331 CITATION_INSERT_PSP = 'PhosphoSitePlus(R) (PSP) was created by Cell Signaling Technology Inc. It is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. When using PSP data or analyses in printed publications or in online resources, the following acknowledgements must be included: (a) the words "PhosphoSitePlus(R), www.phosphosite.org" must be included at appropriate places in the text or webpage, and (b) the following citation must be included in the bibliography: "Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 2015 43:D512-20. PMID: 25514926."'
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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332 CITATION_INSERT_PSP_REF = 'Hornbeck, 2014, "PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.", https://pubmed.ncbi.nlm.nih.gov/22135298, https://doi.org/10.1093/nar/gkr1122'
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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333
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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334 MRGFLTR_METADATA_COLUMNS = [
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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335 "ppep_id",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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336 "Sequence10",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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337 "Sequence7",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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338 "GeneName",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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339 "Phosphoresidue",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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340 "UniProtID",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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341 "Description",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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342 "FunctionPhosphoresidue",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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343 "PutativeUpstreamDomains",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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344 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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345
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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346 # String Constants (end) ############
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347
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348 class Error(Exception):
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349 """Base class for exceptions in this module."""
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350
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351 pass
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352
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353 class PreconditionError(Error):
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354 """Exception raised for errors in the input.
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355
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356 Attributes:
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357 expression -- input expression in which the error occurred
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358 message -- explanation of the error
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359 """
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360
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361 def __init__(self, expression, message):
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362 self.expression = expression
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363 self.message = message
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364
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365 # start_time = time.clock() #timer
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366 start_time = time.process_time() # timer
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367
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368 # get keys from upstream tabular file using readline()
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369 # ref: https://stackoverflow.com/a/16713581/15509512
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370 # answer to "Use codecs to read file with correct encoding"
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371 file1_encoded = open(upstream_map_filename_tab, "rb")
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372 file1 = cx_getreader("latin-1")(file1_encoded)
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373
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374 count = 0
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375 upstream_map_p_peptide_list = []
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376 re_tab = re.compile("^[^\t]*")
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377 while True:
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378 count += 1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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379 # Get next line from file
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380 line = file1.readline()
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381 # if line is empty
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382 # end of file is reached
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383 if not line:
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384 break
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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385 if count > 1:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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386 m = re_tab.match(line)
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387 upstream_map_p_peptide_list.append(m[0])
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388 file1.close()
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389 file1_encoded.close()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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390
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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391 # Get the list of phosphopeptides with the p's that represent the phosphorylation sites removed
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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392 re_phos = re.compile("p")
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393
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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394 end_time = time.process_time() # timer
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395 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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396 "%0.6f pre-read-SwissProt [0.1]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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397 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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398 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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399
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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400 # ----------- Get SwissProt data from SQLite database (start) -----------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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401 # build UniProt sequence LUT and list of unique SwissProt sequences
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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402
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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403 # Open SwissProt SQLite database
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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404 conn = sql.connect(uniprot_sqlite)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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405 cur = conn.cursor()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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406
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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407 # Set up structures to hold SwissProt data
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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408
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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409 uniprot_Sequence_List = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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410 UniProtSeqLUT = {}
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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411
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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412 # Execute query for unique seqs without fetching the results yet
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413 uniprot_unique_seq_cur = cur.execute(UNIPROT_UNIQUE_SEQ_SQL)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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414
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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415 while 1:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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416 batch = uniprot_unique_seq_cur.fetchmany(size=50)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
417 if not batch:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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418 # handle case where no records are returned
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419 break
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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420 for row in batch:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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421 Sequence = row[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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422 UniProtSeqLUT[(Sequence, DESCRIPTION)] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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423 UniProtSeqLUT[(Sequence, GENE_NAME)] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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424 UniProtSeqLUT[(Sequence, UNIPROT_ID)] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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425 UniProtSeqLUT[Sequence] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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426
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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427 # Execute query for seqs and metadata without fetching the results yet
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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428 uniprot_seq_and_meta = cur.execute(UNIPROT_SEQ_AND_META_SQL)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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429
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
430 while 1:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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431 batch = uniprot_seq_and_meta.fetchmany(size=50)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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432 if not batch:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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433 # handle case where no records are returned
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
434 break
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
435 for (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
436 UniProt_ID,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
437 Description,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
438 Gene_Name,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
439 Sequence,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
440 OS,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
441 OX,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
442 PE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
443 SV,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
444 ) in batch:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
445 uniprot_Sequence_List.append(Sequence)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
446 UniProtSeqLUT[Sequence] = Sequence
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
447 UniProtSeqLUT[(Sequence, UNIPROT_ID)].append(UniProt_ID)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
448 UniProtSeqLUT[(Sequence, GENE_NAME)].append(Gene_Name)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
449 if OS != N_A:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
450 Description += " OS=" + OS
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
451 if OX != N_A:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
452 Description += " OX=" + str(int(OX))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
453 if Gene_Name != N_A:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
454 Description += " GN=" + Gene_Name
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
455 if PE != N_A:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
456 Description += " PE=" + PE
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
457 if SV != N_A:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
458 Description += " SV=" + SV
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
459 UniProtSeqLUT[(Sequence, DESCRIPTION)].append(Description)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
460
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
461 # Close SwissProt SQLite database; clean up local variables
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
462 conn.close()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
463 Sequence = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
464 UniProt_ID = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
465 Description = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
466 Gene_Name = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
467
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
468 # ----------- Get SwissProt data from SQLite database (finish) -----------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
469
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
470 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
471 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
472 "%0.6f post-read-SwissProt [0.2]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
473 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
474 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
475
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
476 # ----------- Get SwissProt data from SQLite database (start) -----------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
477 # Open SwissProt SQLite database
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
478 conn = sql.connect(uniprot_sqlite)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
479 cur = conn.cursor()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
480
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
481 # Set up dictionary to aggregate results for phosphopeptides correspounding to dephosphoeptide
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
482 DephosphoPep_UniProtSeq_LUT = {}
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
483
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
484 # Set up dictionary to accumulate results
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
485 PhosphoPep_UniProtSeq_LUT = {}
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
486
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
487 # Execute query for tuples without fetching the results yet
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
488 ppep_pep_uniprotseq_cur = cur.execute(PPEP_PEP_UNIPROTSEQ_SQL)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
489
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
490 while 1:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
491 batch = ppep_pep_uniprotseq_cur.fetchmany(size=50)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
492 if not batch:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
493 # handle case where no records are returned
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
494 break
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
495 for (phospho_pep, dephospho_pep, sequence) in batch:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
496 # do interesting stuff here...
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
497 PhosphoPep_UniProtSeq_LUT[phospho_pep] = phospho_pep
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
498 PhosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
499 (phospho_pep, DEPHOSPHOPEP)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
500 ] = dephospho_pep
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
501 if dephospho_pep not in DephosphoPep_UniProtSeq_LUT:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
502 DephosphoPep_UniProtSeq_LUT[dephospho_pep] = set()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
503 DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
504 (dephospho_pep, DESCRIPTION)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
505 ] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
506 DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
507 (dephospho_pep, GENE_NAME)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
508 ] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
509 DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
510 (dephospho_pep, UNIPROT_ID)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
511 ] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
512 DephosphoPep_UniProtSeq_LUT[(dephospho_pep, SEQUENCE)] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
513 DephosphoPep_UniProtSeq_LUT[dephospho_pep].add(phospho_pep)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
514
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
515 if (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
516 sequence
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
517 not in DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
518 (dephospho_pep, SEQUENCE)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
519 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
520 ):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
521 DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
522 (dephospho_pep, SEQUENCE)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
523 ].append(sequence)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
524 for phospho_pep in DephosphoPep_UniProtSeq_LUT[dephospho_pep]:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
525 if phospho_pep != phospho_pep:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
526 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
527 "phospho_pep:'%s' phospho_pep:'%s'"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
528 % (phospho_pep, phospho_pep)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
529 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
530 if phospho_pep not in PhosphoPep_UniProtSeq_LUT:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
531 PhosphoPep_UniProtSeq_LUT[phospho_pep] = phospho_pep
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
532 PhosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
533 (phospho_pep, DEPHOSPHOPEP)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
534 ] = dephospho_pep
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
535 r = list(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
536 zip(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
537 [s for s in UniProtSeqLUT[(sequence, UNIPROT_ID)]],
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
538 [s for s in UniProtSeqLUT[(sequence, GENE_NAME)]],
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
539 [
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
540 s
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
541 for s in UniProtSeqLUT[(sequence, DESCRIPTION)]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
542 ],
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
543 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
544 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
545 # Sort by `UniProt_ID`
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
546 # ref: https://stackoverflow.com/a/4174955/15509512
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
547 r = sorted(r, key=operator.itemgetter(0))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
548 # Get one tuple for each `phospho_pep`
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
549 # in DephosphoPep_UniProtSeq_LUT[dephospho_pep]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
550 for (upid, gn, desc) in r:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
551 # Append pseudo-tuple per UniProt_ID but only when it is not present
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
552 if (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
553 upid
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
554 not in DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
555 (dephospho_pep, UNIPROT_ID)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
556 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
557 ):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
558 DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
559 (dephospho_pep, UNIPROT_ID)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
560 ].append(upid)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
561 DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
562 (dephospho_pep, DESCRIPTION)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
563 ].append(desc)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
564 DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
565 (dephospho_pep, GENE_NAME)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
566 ].append(gn)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
567
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
568 # Close SwissProt SQLite database; clean up local variables
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
569 conn.close()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
570 # wipe local variables
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
571 phospho_pep = dephospho_pep = sequence = 0
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
572 upid = gn = desc = r = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
573
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
574 # ----------- Get SwissProt data from SQLite database (finish) -----------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
575
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
576 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
577 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
578 "%0.6f finished reading and decoding '%s' [0.4]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
579 % (end_time - start_time, upstream_map_filename_tab),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
580 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
581 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
582
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
583 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
584 "{:>10} unique upstream phosphopeptides tested".format(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
585 str(len(upstream_map_p_peptide_list))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
586 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
587 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
588
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
589 # Read in Upstream tabular file
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
590 # We are discarding the intensity data; so read it as text
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
591 upstream_data = pandas.read_table(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
592 upstream_map_filename_tab, dtype="str", index_col=0
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
593 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
594
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
595 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
596 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
597 "%0.6f read Upstream Map from file [1g_1]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
598 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
599 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
600 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
601
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
602 upstream_data.index = upstream_map_p_peptide_list
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
603
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
604 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
605 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
606 "%0.6f added index to Upstream Map [1g_2]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
607 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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608 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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609 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
610
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
611 # trim upstream_data to include only the upstream map columns
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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612 old_cols = upstream_data.columns.tolist()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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613 i = 0
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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614 first_intensity = -1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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615 last_intensity = -1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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616 intensity_re = re.compile("Intensity.*")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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617 for col_name in old_cols:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
618 m = intensity_re.match(col_name)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
619 if m:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
620 last_intensity = i
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
621 if first_intensity == -1:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
622 first_intensity = i
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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623 i += 1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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624 # print('last intensity = %d' % last_intensity)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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625 col_PKCalpha = last_intensity + 2
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
626
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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627 data_in_cols = [old_cols[0]] + old_cols[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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628 first_intensity: last_intensity + 1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
629 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
630
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
631 if upstream_data.empty:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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632 print("upstream_data is empty")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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633 exit(0)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
634
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
635 data_in = upstream_data.copy(deep=True)[data_in_cols]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
636
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
637 # Convert floating-point integers to int64 integers
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
638 # ref: https://stackoverflow.com/a/68497603/15509512
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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639 data_in[list(data_in.columns[1:])] = (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
640 data_in[list(data_in.columns[1:])]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
641 .astype("float64")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
642 .apply(np.int64)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
643 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
644
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
645 # create another phosphopeptide column that will be used to join later;
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
646 # MAY need to change depending on Phosphopeptide column position
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
647 # data_in[PHOSPHOPEPTIDE_MATCH] = data_in[data_in.columns.tolist()[0]]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
648 data_in[PHOSPHOPEPTIDE_MATCH] = data_in.index
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
649
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
650 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
651 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
652 "%0.6f set data_in[PHOSPHOPEPTIDE_MATCH] [A]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
653 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
654 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
655 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
656
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
657 # Produce a dictionary of metadata for a single phosphopeptide.
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
658 # This is a replacement of `UniProtInfo_subdict` in the original code.
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
659 def pseq_to_subdict(phospho_pep):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
660 # Strip "p" from phosphopeptide sequence
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
661 dephospho_pep = re_phos.sub("", phospho_pep)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
662
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
663 # Determine number of phosphoresidues in phosphopeptide
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
664 numps = len(phospho_pep) - len(dephospho_pep)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
665
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
666 # Determine location(s) of phosphoresidue(s) in phosphopeptide
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
667 # (used later for Phosphoresidue, Sequence7, and Sequence10)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
668 ploc = [] # list of p locations
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
669 i = 0
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
670 p = phospho_pep
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
671 while i < numps:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
672 ploc.append(p.find("p"))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
673 p = p[: p.find("p")] + p[p.find("p") + 1:]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
674 i += 1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
675
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
676 # Establish nested dictionary
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
677 result = {}
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
678 result[SEQUENCE] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
679 result[UNIPROT_ID] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
680 result[DESCRIPTION] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
681 result[GENE_NAME] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
682 result[PHOSPHORESIDUE] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
683 result[SEQUENCE7] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
684 result[SEQUENCE10] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
685
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
686 # Add stripped sequence to dictionary
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
687 result[SEQUENCE].append(dephospho_pep)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
688
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
689 # Locate phospho_pep in PhosphoPep_UniProtSeq_LUT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
690 # Caller may elect to:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
691 # try:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
692 # ...
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
693 # except PreconditionError as pe:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
694 # print("'{expression}': {message}".format(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
695 # expression = pe.expression,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
696 # message = pe.message))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
697 # )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
698 # )
6
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
699 if phospho_pep not in PhosphoPep_UniProtSeq_LUT:
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
700 raise PreconditionError(
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
701 phospho_pep,
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
702 "no matching phosphopeptide found in PhosphoPep_UniProtSeq_LUT",
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
703 )
5
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
704 if dephospho_pep not in DephosphoPep_UniProtSeq_LUT:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
705 raise PreconditionError(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
706 dephospho_pep,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
707 "dephosphorylated phosphopeptide not found in DephosphoPep_UniProtSeq_LUT",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
708 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
709 if (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
710 dephospho_pep
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
711 != PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
712 ):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
713 raise PreconditionError(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
714 dephospho_pep,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
715 "dephosphorylated phosphopeptide does not match "
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
716 + "PhosphoPep_UniProtSeq_LUT[(phospho_pep,DEPHOSPHOPEP)] = "
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
717 + PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)],
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
718 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
719 result[SEQUENCE] = [dephospho_pep]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
720 result[UNIPROT_ID] = DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
721 (dephospho_pep, UNIPROT_ID)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
722 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
723 result[DESCRIPTION] = DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
724 (dephospho_pep, DESCRIPTION)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
725 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
726 result[GENE_NAME] = DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
727 (dephospho_pep, GENE_NAME)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
728 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
729 if (dephospho_pep, SEQUENCE) not in DephosphoPep_UniProtSeq_LUT:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
730 raise PreconditionError(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
731 dephospho_pep,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
732 "no matching phosphopeptide found in DephosphoPep_UniProtSeq_LUT",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
733 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
734 UniProtSeqList = DephosphoPep_UniProtSeq_LUT[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
735 (dephospho_pep, SEQUENCE)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
736 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
737 if len(UniProtSeqList) < 1:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
738 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
739 "Skipping DephosphoPep_UniProtSeq_LUT[('%s',SEQUENCE)] because value has zero length"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
740 % dephospho_pep
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
741 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
742 # raise PreconditionError(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
743 # "DephosphoPep_UniProtSeq_LUT[('" + dephospho_pep + ",SEQUENCE)",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
744 # 'value has zero length'
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
745 # )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
746 for UniProtSeq in UniProtSeqList:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
747 i = 0
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
748 phosphoresidues = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
749 seq7s_set = set()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
750 seq7s = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
751 seq10s_set = set()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
752 seq10s = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
753 while i < len(ploc):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
754 start = UniProtSeq.find(dephospho_pep)
6
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
755 # handle case where no sequence was found for dep-pep
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
756 if start < 0:
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
757 i += 1
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
758 continue
5
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
759 psite = (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
760 start + ploc[i]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
761 ) # location of phosphoresidue on protein sequence
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
762
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
763 # add Phosphoresidue
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
764 phosphosite = "p" + str(UniProtSeq)[psite] + str(psite + 1)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
765 phosphoresidues.append(phosphosite)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
766
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
767 # Add Sequence7
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
768 if psite < 7: # phospho_pep at N terminus
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
769 seq7 = str(UniProtSeq)[: psite + 8]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
770 if seq7[psite] == "S": # if phosphosresidue is serine
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
771 pres = "s"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
772 elif (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
773 seq7[psite] == "T"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
774 ): # if phosphosresidue is threonine
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
775 pres = "t"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
776 elif (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
777 seq7[psite] == "Y"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
778 ): # if phosphoresidue is tyrosine
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
779 pres = "y"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
780 else: # if not pSTY
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
781 pres = "?"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
782 seq7 = (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
783 seq7[:psite] + pres + seq7[psite + 1: psite + 8]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
784 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
785 while (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
786 len(seq7) < 15
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
787 ): # add appropriate number of "_" to the front
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
788 seq7 = "_" + seq7
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
789 elif (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
790 len(UniProtSeq) - psite < 8
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
791 ): # phospho_pep at C terminus
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
792 seq7 = str(UniProtSeq)[psite - 7:]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
793 if seq7[7] == "S":
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
794 pres = "s"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
795 elif seq7[7] == "T":
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
796 pres = "t"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
797 elif seq7[7] == "Y":
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
798 pres = "y"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
799 else:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
800 pres = "?"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
801 seq7 = seq7[:7] + pres + seq7[8:]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
802 while (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
803 len(seq7) < 15
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
804 ): # add appropriate number of "_" to the back
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
805 seq7 = seq7 + "_"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
806 else:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
807 seq7 = str(UniProtSeq)[psite - 7: psite + 8]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
808 pres = "" # phosphoresidue
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
809 if seq7[7] == "S": # if phosphosresidue is serine
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
810 pres = "s"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
811 elif seq7[7] == "T": # if phosphosresidue is threonine
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
812 pres = "t"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
813 elif seq7[7] == "Y": # if phosphoresidue is tyrosine
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
814 pres = "y"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
815 else: # if not pSTY
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
816 pres = "?"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
817 seq7 = seq7[:7] + pres + seq7[8:]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
818 if seq7 not in seq7s_set:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
819 seq7s.append(seq7)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
820 seq7s_set.add(seq7)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
821
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
822 # add Sequence10
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
823 if psite < 10: # phospho_pep at N terminus
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
824 seq10 = (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
825 str(UniProtSeq)[:psite]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
826 + "p"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
827 + str(UniProtSeq)[psite: psite + 11]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
828 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
829 elif (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
830 len(UniProtSeq) - psite < 11
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
831 ): # phospho_pep at C terminus
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
832 seq10 = (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
833 str(UniProtSeq)[psite - 10: psite]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
834 + "p"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
835 + str(UniProtSeq)[psite:]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
836 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
837 else:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
838 seq10 = str(UniProtSeq)[psite - 10: psite + 11]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
839 seq10 = seq10[:10] + "p" + seq10[10:]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
840 if seq10 not in seq10s_set:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
841 seq10s.append(seq10)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
842 seq10s_set.add(seq10)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
843
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
844 i += 1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
845
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
846 result[PHOSPHORESIDUE].append(phosphoresidues)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
847 result[SEQUENCE7].append(seq7s)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
848 # result[SEQUENCE10] is a list of lists of strings
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
849 result[SEQUENCE10].append(seq10s)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
850
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
851 r = list(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
852 zip(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
853 result[UNIPROT_ID],
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
854 result[GENE_NAME],
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
855 result[DESCRIPTION],
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
856 result[PHOSPHORESIDUE],
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
857 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
858 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
859 # Sort by `UniProt_ID`
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
860 # ref: https://stackoverflow.com//4174955/15509512
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
861 s = sorted(r, key=operator.itemgetter(0))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
862
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
863 result[UNIPROT_ID] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
864 result[GENE_NAME] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
865 result[DESCRIPTION] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
866 result[PHOSPHORESIDUE] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
867
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
868 for r in s:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
869 result[UNIPROT_ID].append(r[0])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
870 result[GENE_NAME].append(r[1])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
871 result[DESCRIPTION].append(r[2])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
872 result[PHOSPHORESIDUE].append(r[3])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
873
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
874 # convert lists to strings in the dictionary
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
875 for key, value in result.items():
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
876 if key not in [PHOSPHORESIDUE, SEQUENCE7, SEQUENCE10]:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
877 result[key] = "; ".join(map(str, value))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
878 elif key in [SEQUENCE10]:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
879 # result[SEQUENCE10] is a list of lists of strings
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
880 joined_value = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
881 joined_set = set()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
882 sep = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
883 for valL in value:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
884 # valL is a list of strings
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
885 for val in valL:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
886 # val is a string
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
887 if val not in joined_set:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
888 joined_set.add(val)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
889 joined_value += sep + val
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
890 sep = "; "
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
891 # joined_value is a string
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
892 result[key] = joined_value
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
893
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
894 newstring = "; ".join(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
895 [", ".join(prez) for prez in result[PHOSPHORESIDUE]]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
896 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
897 # #separate the isoforms in PHOSPHORESIDUE column with ";"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
898 # oldstring = result[PHOSPHORESIDUE]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
899 # oldlist = list(oldstring)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
900 # newstring = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
901 # i = 0
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
902 # for e in oldlist:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
903 # if e == ";":
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
904 # if numps > 1:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
905 # if i%numps:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
906 # newstring = newstring + ";"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
907 # else:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
908 # newstring = newstring + ","
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
909 # else:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
910 # newstring = newstring + ";"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
911 # i +=1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
912 # else:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
913 # newstring = newstring + e
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
914 result[PHOSPHORESIDUE] = newstring
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
915
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
916 # separate sequence7's by |
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
917 oldstring = result[SEQUENCE7]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
918 oldlist = oldstring
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
919 newstring = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
920 for ol in oldlist:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
921 for e in ol:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
922 if e == ";":
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
923 newstring = newstring + " |"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
924 elif len(newstring) > 0 and 1 > newstring.count(e):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
925 newstring = newstring + " | " + e
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
926 elif 1 > newstring.count(e):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
927 newstring = newstring + e
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
928 result[SEQUENCE7] = newstring
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
929
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
930 return [phospho_pep, result]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
931
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
932 # Construct list of [string, dictionary] lists
6
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
933 # where the dictionary provides the SwissProt metadata
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
934 # for a phosphopeptide
5
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
935 result_list = [
6
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
936 whine(pseq_to_subdict, psequence)
5
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
937 for psequence in data_in[PHOSPHOPEPTIDE_MATCH]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
938 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
939
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
940 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
941 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
942 "%0.6f added SwissProt annotations to phosphopeptides [B]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
943 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
944 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
945 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
946
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
947 # Construct dictionary from list of lists
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
948 # ref: https://www.8bitavenue.com/how-to-convert-list-of-lists-to-dictionary-in-python/
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
949 UniProt_Info = {
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
950 result[0]: result[1]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
951 for result in result_list
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
952 if result is not None
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
953 }
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
954
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
955 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
956 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
957 "%0.6f create dictionary mapping phosphopeptide to metadata dictionary [C]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
958 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
959 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
960 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
961
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
962 # cosmetic: add N_A to phosphopeptide rows with no hits
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
963 p_peptide_list = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
964 for key in UniProt_Info:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
965 p_peptide_list.append(key)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
966 for nestedKey in UniProt_Info[key]:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
967 if UniProt_Info[key][nestedKey] == "":
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
968 UniProt_Info[key][nestedKey] = N_A
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
969
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
970 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
971 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
972 "%0.6f performed cosmetic clean-up [D]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
973 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
974 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
975
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
976 # convert UniProt_Info dictionary to dataframe
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
977 uniprot_df = pandas.DataFrame.transpose(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
978 pandas.DataFrame.from_dict(UniProt_Info)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
979 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
980
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
981 # reorder columns to match expected output file
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
982 uniprot_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
983 PHOSPHOPEPTIDE
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
984 ] = uniprot_df.index # make index a column too
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
985
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
986 cols = uniprot_df.columns.tolist()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
987 # cols = [cols[-1]]+cols[4:6]+[cols[1]]+[cols[2]]+[cols[6]]+[cols[0]]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
988 # uniprot_df = uniprot_df[cols]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
989 uniprot_df = uniprot_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
990 [
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
991 PHOSPHOPEPTIDE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
992 SEQUENCE10,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
993 SEQUENCE7,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
994 GENE_NAME,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
995 PHOSPHORESIDUE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
996 UNIPROT_ID,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
997 DESCRIPTION,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
998 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
999 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1000
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1001 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1002 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1003 "%0.6f reordered columns to match expected output file [1]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1004 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1005 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1006 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1007
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1008 # concat to split then groupby to collapse
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1009 seq7_df = pandas.concat(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1010 [
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1011 pandas.Series(row[PHOSPHOPEPTIDE], row[SEQUENCE7].split(" | "))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1012 for _, row in uniprot_df.iterrows()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1013 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1014 ).reset_index()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1015 seq7_df.columns = [SEQUENCE7, PHOSPHOPEPTIDE]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1016
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1017 # --- -------------- begin read PSP_Regulatory_sites ---------------------------------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1018 # read in PhosphoSitePlus Regulatory Sites dataset
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1019 # ----------- Get PhosphoSitePlus Regulatory Sites data from SQLite database (start) -----------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1020 conn = sql.connect(uniprot_sqlite)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1021 regsites_df = pandas.read_sql_query(PSP_REGSITE_SQL, conn)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1022 # Close SwissProt SQLite database
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1023 conn.close()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1024 # ... -------------- end read PSP_Regulatory_sites ------------------------------------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1025
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1026 # keep only the human entries in dataframe
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1027 if len(species) > 0:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1028 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1029 'Limit PhosphoSitesPlus records to species "' + species + '"'
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1030 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1031 regsites_df = regsites_df[regsites_df.ORGANISM == species]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1032
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1033 # merge the seq7 df with the regsites df based off of the sequence7
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1034 merge_df = seq7_df.merge(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1035 regsites_df,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1036 left_on=SEQUENCE7,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1037 right_on=SITE_PLUSMINUS_7AA_SQL,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1038 how="left",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1039 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1040
6
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
1041 # after merging df, select only the columns of interest;
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
1042 # note that PROTEIN is absent here
5
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1043 merge_df = merge_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1044 [
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1045 PHOSPHOPEPTIDE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1046 SEQUENCE7,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1047 ON_FUNCTION,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1048 ON_PROCESS,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1049 ON_PROT_INTERACT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1050 ON_OTHER_INTERACT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1051 ON_NOTES,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1052 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1053 ]
6
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
1054 # combine column values of interest
922d309640db "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
1055 # into one FUNCTION_PHOSPHORESIDUE column"
5
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1056 merge_df[FUNCTION_PHOSPHORESIDUE] = merge_df[ON_FUNCTION].str.cat(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1057 merge_df[ON_PROCESS], sep="; ", na_rep=""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1058 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1059 merge_df[FUNCTION_PHOSPHORESIDUE] = merge_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1060 FUNCTION_PHOSPHORESIDUE
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1061 ].str.cat(merge_df[ON_PROT_INTERACT], sep="; ", na_rep="")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1062 merge_df[FUNCTION_PHOSPHORESIDUE] = merge_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1063 FUNCTION_PHOSPHORESIDUE
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1064 ].str.cat(merge_df[ON_OTHER_INTERACT], sep="; ", na_rep="")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1065 merge_df[FUNCTION_PHOSPHORESIDUE] = merge_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1066 FUNCTION_PHOSPHORESIDUE
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1067 ].str.cat(merge_df[ON_NOTES], sep="; ", na_rep="")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1068
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1069 # remove the columns that were combined
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1070 merge_df = merge_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1071 [PHOSPHOPEPTIDE, SEQUENCE7, FUNCTION_PHOSPHORESIDUE]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1072 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1073
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1074 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1075 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1076 "%0.6f merge regsite metadata [1a]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1077 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1078 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1079
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1080 # cosmetic changes to Function Phosphoresidue column
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1081 fp_series = pandas.Series(merge_df[FUNCTION_PHOSPHORESIDUE])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1082
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1083 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1084 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1085 "%0.6f more cosmetic changes [1b]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1086 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1087 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1088
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1089 i = 0
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1090 while i < len(fp_series):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1091 # remove the extra ";" so that it looks more professional
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1092 if fp_series[i] == "; ; ; ; ": # remove ; from empty hits
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1093 fp_series[i] = ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1094 while fp_series[i].endswith("; "): # remove ; from the ends
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1095 fp_series[i] = fp_series[i][:-2]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1096 while fp_series[i].startswith("; "): # remove ; from the beginning
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1097 fp_series[i] = fp_series[i][2:]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1098 fp_series[i] = fp_series[i].replace("; ; ; ; ", "; ")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1099 fp_series[i] = fp_series[i].replace("; ; ; ", "; ")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1100 fp_series[i] = fp_series[i].replace("; ; ", "; ")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1101
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1102 # turn blanks into N_A to signify the info was searched for but cannot be found
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1103 if fp_series[i] == "":
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1104 fp_series[i] = N_A
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1105
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1106 i += 1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1107 merge_df[FUNCTION_PHOSPHORESIDUE] = fp_series
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1108
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1109 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1110 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1111 "%0.6f cleaned up semicolons [1c]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1112 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1113 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1114
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1115 # merge uniprot df with merge df
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1116 uniprot_regsites_merged_df = uniprot_df.merge(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1117 merge_df,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1118 left_on=PHOSPHOPEPTIDE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1119 right_on=PHOSPHOPEPTIDE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1120 how="left",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1121 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1122
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1123 # collapse the merged df
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1124 uniprot_regsites_collapsed_df = pandas.DataFrame(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1125 uniprot_regsites_merged_df.groupby(PHOSPHOPEPTIDE)[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1126 FUNCTION_PHOSPHORESIDUE
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1127 ].apply(lambda x: ppep_join(x))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1128 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1129 # .apply(lambda x: "%s" % ' | '.join(x)))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1130
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1131 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1132 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1133 "%0.6f collapsed pandas dataframe [1d]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1134 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1135 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1136
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1137 uniprot_regsites_collapsed_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1138 PHOSPHOPEPTIDE
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1139 ] = (
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1140 uniprot_regsites_collapsed_df.index
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1141 ) # add df index as its own column
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1142
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1143 # rename columns
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1144 uniprot_regsites_collapsed_df.columns = [
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1145 FUNCTION_PHOSPHORESIDUE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1146 "ppp",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1147 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1148
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1149 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1150 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1151 "%0.6f selected columns to be merged to uniprot_df [1e]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1152 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1153 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1154 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1155
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1156 # add columns based on Sequence7 matching site_+/-7_AA
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1157 uniprot_regsite_df = pandas.merge(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1158 left=uniprot_df,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1159 right=uniprot_regsites_collapsed_df,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1160 how="left",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1161 left_on=PHOSPHOPEPTIDE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1162 right_on="ppp",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1163 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1164
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1165 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1166 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1167 "%0.6f added columns based on Sequence7 matching site_+/-7_AA [1f]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1168 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1169 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1170 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1171
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1172 data_in.rename(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1173 {"Protein description": PHOSPHOPEPTIDE},
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1174 axis="columns",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1175 inplace=True,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1176 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1177
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1178 # data_in.sort_values(PHOSPHOPEPTIDE_MATCH, inplace=True, kind='mergesort')
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1179 res2 = sorted(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1180 data_in[PHOSPHOPEPTIDE_MATCH].tolist(), key=lambda s: s.casefold()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1181 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1182 data_in = data_in.loc[res2]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1183
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1184 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1185 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1186 "%0.6f sorting time [1f]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1187 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1188 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1189
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1190 cols = [old_cols[0]] + old_cols[col_PKCalpha - 1:]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1191 upstream_data = upstream_data[cols]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1192
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1193 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1194 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1195 "%0.6f refactored columns for Upstream Map [1g]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1196 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1197 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1198 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1199
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1200 # #rename upstream columns in new list
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1201 # new_cols = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1202 # for name in cols:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1203 # if "_NetworKIN" in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1204 # name = name.split("_")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1205 # if " motif" in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1206 # name = name.split(" motif")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1207 # if " sequence " in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1208 # name = name.split(" sequence")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1209 # if "_Phosida" in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1210 # name = name.split("_")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1211 # if "_PhosphoSite" in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1212 # name = name.split("_")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1213 # new_cols.append(name)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1214
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1215 # rename upstream columns in new list
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1216 def col_rename(name):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1217 if "_NetworKIN" in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1218 name = name.split("_")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1219 if " motif" in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1220 name = name.split(" motif")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1221 if " sequence " in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1222 name = name.split(" sequence")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1223 if "_Phosida" in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1224 name = name.split("_")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1225 if "_PhosphoSite" in name:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1226 name = name.split("_")[0]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1227 return name
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1228
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1229 new_cols = [col_rename(col) for col in cols]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1230 upstream_data.columns = new_cols
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1231
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1232 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1233 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1234 "%0.6f renamed columns for Upstream Map [1h_1]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1235 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1236 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1237 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1238
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1239 # Create upstream_data_cast as a copy of upstream_data
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1240 # but with first column substituted by the phosphopeptide sequence
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1241 upstream_data_cast = upstream_data.copy()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1242 new_cols_cast = new_cols
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1243 new_cols_cast[0] = "p_peptide"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1244 upstream_data_cast.columns = new_cols_cast
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1245 upstream_data_cast["p_peptide"] = upstream_data.index
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1246
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1247 # --- -------------- begin read upstream_data_melt ------------------------------------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1248 # ----------- Get melted kinase mapping data from SQLite database (start) -----------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1249 conn = sql.connect(uniprot_sqlite)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1250 upstream_data_melt_df = pandas.read_sql_query(PPEP_MELT_SQL, conn)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1251 # Close SwissProt SQLite database
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1252 conn.close()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1253 upstream_data_melt = upstream_data_melt_df.copy()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1254 upstream_data_melt.columns = ["p_peptide", "characterization", "X"]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1255 upstream_data_melt["characterization"] = [
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1256 col_rename(s) for s in upstream_data_melt["characterization"]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1257 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1258
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1259 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1260 "%0.6f upstream_data_melt_df initially has %d rows"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1261 % (end_time - start_time, len(upstream_data_melt.axes[0])),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1262 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1263 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1264 # ref: https://stackoverflow.com/a/27360130/15509512
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1265 # e.g. df.drop(df[df.score < 50].index, inplace=True)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1266 upstream_data_melt.drop(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1267 upstream_data_melt[upstream_data_melt.X != "X"].index, inplace=True
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1268 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1269 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1270 "%0.6f upstream_data_melt_df pre-dedup has %d rows"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1271 % (end_time - start_time, len(upstream_data_melt.axes[0])),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1272 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1273 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1274 # ----------- Get melted kinase mapping data from SQLite database (finish) -----------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1275 # ... -------------- end read upstream_data_melt --------------------------------------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1276
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1277 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1278 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1279 "%0.6f melted and minimized Upstream Map dataframe [1h_2]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1280 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1281 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1282 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1283 # ... end read upstream_data_melt
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1284
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1285 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1286 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1287 "%0.6f indexed melted Upstream Map [1h_2a]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1288 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1289 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1290 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1291
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1292 upstream_delta_melt_LoL = upstream_data_melt.values.tolist()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1293
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1294 melt_dict = {}
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1295 for key in upstream_map_p_peptide_list:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1296 melt_dict[key] = []
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1297
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1298 for el in upstream_delta_melt_LoL:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1299 (p_peptide, characterization, X) = tuple(el)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1300 if p_peptide in melt_dict:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1301 melt_dict[p_peptide].append(characterization)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1302 else:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1303 exit(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1304 'Phosphopeptide %s not found in ppep_mapping_db: "phopsphopeptides" and "ppep_mapping_db" must both originate from the same run of mqppep_kinase_mapping'
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1305 % (p_peptide)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1306 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1307
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1308 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1309 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1310 "%0.6f appended peptide characterizations [1h_2b]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1311 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1312 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1313 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1314
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1315 # for key in upstream_map_p_peptide_list:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1316 # melt_dict[key] = ' | '.join(melt_dict[key])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1317
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1318 for key in upstream_map_p_peptide_list:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1319 melt_dict[key] = melt_join(melt_dict[key])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1320
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1321 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1322 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1323 "%0.6f concatenated multiple characterizations [1h_2c]"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1324 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1325 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1326 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1327
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1328 # map_dict is a dictionary of dictionaries
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1329 map_dict = {}
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1330 for key in upstream_map_p_peptide_list:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1331 map_dict[key] = {}
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1332 map_dict[key][PUTATIVE_UPSTREAM_DOMAINS] = melt_dict[key]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1333
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1334 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1335 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1336 "%0.6f instantiated map dictionary [2]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1337 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1338 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1339
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1340 # convert map_dict to dataframe
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1341 map_df = pandas.DataFrame.transpose(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1342 pandas.DataFrame.from_dict(map_dict)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1343 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1344 map_df["p-peptide"] = map_df.index # make index a column too
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1345 cols_map_df = map_df.columns.tolist()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1346 cols_map_df = [cols_map_df[1]] + [cols_map_df[0]]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1347 map_df = map_df[cols_map_df]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1348
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1349 # join map_df to uniprot_regsite_df
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1350 output_df = uniprot_regsite_df.merge(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1351 map_df, how="left", left_on=PHOSPHOPEPTIDE, right_on="p-peptide"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1352 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1353
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1354 output_df = output_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1355 [
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1356 PHOSPHOPEPTIDE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1357 SEQUENCE10,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1358 SEQUENCE7,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1359 GENE_NAME,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1360 PHOSPHORESIDUE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1361 UNIPROT_ID,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1362 DESCRIPTION,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1363 FUNCTION_PHOSPHORESIDUE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1364 PUTATIVE_UPSTREAM_DOMAINS,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1365 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1366 ]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1367
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1368 # cols_output_prelim = output_df.columns.tolist()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1369 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1370 # print("cols_output_prelim")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1371 # print(cols_output_prelim)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1372 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1373 # cols_output = cols_output_prelim[:8]+[cols_output_prelim[9]]+[cols_output_prelim[10]]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1374 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1375 # print("cols_output with p-peptide")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1376 # print(cols_output)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1377 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1378 # cols_output = [col for col in cols_output if not col == "p-peptide"]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1379 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1380 # print("cols_output")
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1381 # print(cols_output)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1382 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
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diff changeset
1383 # output_df = output_df[cols_output]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
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diff changeset
1384
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
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diff changeset
1385 # join output_df back to quantitative columns in data_in df
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
1386 quant_cols = data_in.columns.tolist()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
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diff changeset
1387 quant_cols = quant_cols[1:]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
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diff changeset
1388 quant_data = data_in[quant_cols]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1389
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1390 # ----------- Write merge/filter metadata to SQLite database (start) -----------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1391 # Open SwissProt SQLite database
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
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diff changeset
1392 conn = sql.connect(output_sqlite)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
1393 cur = conn.cursor()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1394
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1395 cur.executescript(MRGFLTR_DDL)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1396
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1397 cur.execute(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1398 CITATION_INSERT_STMT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1399 ("mrgfltr_metadata_view", CITATION_INSERT_PSP),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1400 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1401 cur.execute(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1402 CITATION_INSERT_STMT, ("mrgfltr_metadata", CITATION_INSERT_PSP)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1403 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1404 cur.execute(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1405 CITATION_INSERT_STMT,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1406 ("mrgfltr_metadata_view", CITATION_INSERT_PSP_REF),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1407 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1408 cur.execute(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1409 CITATION_INSERT_STMT, ("mrgfltr_metadata", CITATION_INSERT_PSP_REF)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1410 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1411
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1412 # Read ppep-to-sequence LUT
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1413 ppep_lut_df = pandas.read_sql_query(PPEP_ID_SQL, conn)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1414 # write only metadata for merged/filtered records to SQLite
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1415 mrgfltr_metadata_df = output_df.copy()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1416 # replace phosphopeptide seq with ppep.id
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1417 mrgfltr_metadata_df = ppep_lut_df.merge(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1418 mrgfltr_metadata_df,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1419 left_on="ppep_seq",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1420 right_on=PHOSPHOPEPTIDE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1421 how="inner",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1422 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1423 mrgfltr_metadata_df.drop(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1424 columns=[PHOSPHOPEPTIDE, "ppep_seq"], inplace=True
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1425 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1426 # rename columns
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1427 mrgfltr_metadata_df.columns = MRGFLTR_METADATA_COLUMNS
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1428 mrgfltr_metadata_df.to_sql(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1429 "mrgfltr_metadata",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1430 con=conn,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1431 if_exists="append",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1432 index=False,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1433 method="multi",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1434 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1435
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1436 # Close SwissProt SQLite database
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1437 conn.close()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1438 # ----------- Write merge/filter metadata to SQLite database (finish) -----------
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1439
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1440 output_df = output_df.merge(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1441 quant_data,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1442 how="right",
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1443 left_on=PHOSPHOPEPTIDE,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1444 right_on=PHOSPHOPEPTIDE_MATCH,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1445 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1446 output_cols = output_df.columns.tolist()
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1447 output_cols = output_cols[:-1]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1448 output_df = output_df[output_cols]
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1449
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1450 # cosmetic changes to Upstream column
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1451 output_df[PUTATIVE_UPSTREAM_DOMAINS] = output_df[
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1452 PUTATIVE_UPSTREAM_DOMAINS
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1453 ].fillna(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1454 ""
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1455 ) # fill the NaN with "" for those Phosphopeptides that got a "WARNING: Failed match for " in the upstream mapping
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1456 us_series = pandas.Series(output_df[PUTATIVE_UPSTREAM_DOMAINS])
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1457 i = 0
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1458 while i < len(us_series):
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1459 # turn blanks into N_A to signify the info was searched for but cannot be found
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1460 if us_series[i] == "":
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1461 us_series[i] = N_A
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1462 i += 1
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1463 output_df[PUTATIVE_UPSTREAM_DOMAINS] = us_series
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1464
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1465 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1466 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1467 "%0.6f establisheed output [3]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1468 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1469 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1470
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1471 (output_rows, output_cols) = output_df.shape
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1472
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1473 output_df = output_df.convert_dtypes(convert_integer=True)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1474
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1475 # Output onto Final CSV file
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
1476 output_df.to_csv(output_filename_csv, index=False)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1477 output_df.to_csv(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1478 output_filename_tab, quoting=None, sep="\t", index=False
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1479 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1480
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1481 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1482 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1483 "%0.6f wrote output [4]" % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1484 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1485 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1486
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1487 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1488 "{:>10} phosphopeptides written to output".format(str(output_rows))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1489 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1490
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1491 end_time = time.process_time() # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1492 print(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1493 "%0.6f seconds of non-system CPU time were consumed"
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1494 % (end_time - start_time,),
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1495 file=sys.stderr,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1496 ) # timer
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1497
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1498 # Rev. 7/1/2016
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1499 # Rev. 7/3/2016 : fill NaN in Upstream column to replace to N/A's
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1500 # Rev. 7/3/2016: renamed Upstream column to PUTATIVE_UPSTREAM_DOMAINS
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1501 # Rev. 12/2/2021: Converted to Python from ipynb; use fast Aho-Corasick searching; \
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1502 # read from SwissProt SQLite database
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1503 # Rev. 12/9/2021: Transfer code to Galaxy tool wrapper
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1504
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1505 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
1506 # copied from Excel Output Script.ipynb END #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1507 #
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1508
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1509 try:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1510 catch(
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1511 mqpep_getswissprot,
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1512 )
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1513 exit(0)
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1514 except Exception as e:
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
1515 exit("Internal error running mqpep_getswissprot(): %s" % (e))
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
1516
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
1517
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
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diff changeset
1518 if __name__ == "__main__":
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
1519 __main__()