Mercurial > repos > eschen42 > mqppep_anova

annotate search_ppep.py @ 23:3911581e639a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
author eschen42
date Mon, 11 Jul 2022 13:51:14 +0000
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3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1 #!/usr/bin/env python
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2 # Search and memoize phosphopeptides in Swiss-Prot SQLite table UniProtKB
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3
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4 import argparse
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5 import os.path
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6 import re
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7 import sqlite3
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8 import sys # import the sys module for exc_info
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9 import time
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10 import traceback # import the traceback module for format_exception
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11 from codecs import getreader as cx_getreader
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12
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13 # For Aho-Corasick search for fixed set of substrings
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14 # - add_word
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15 # - make_automaton
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16 # - iter
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17 import ahocorasick
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18
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20 # ref: https://stackoverflow.com/a/8915613/15509512
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21 # answers: "How to handle exceptions in a list comprehensions"
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22 # usage:
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23 # from math import log
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24 # eggs = [1,3,0,3,2]
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25 # print([x for x in [catch(log, egg) for egg in eggs] if x is not None])
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26 # producing:
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27 # for <built-in function log>
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28 # with args (0,)
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29 # exception: math domain error
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30 # [0.0, 1.0986122886681098, 1.0986122886681098, 0.6931471805599453]
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31 def catch(func, *args, handle=lambda e: e, **kwargs):
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32
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33 try:
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34 return func(*args, **kwargs)
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35 except Exception as e:
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36 print("For %s" % str(func))
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37 print(" with args %s" % str(args))
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38 print(" caught exception: %s" % str(e))
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39 (ty, va, tb) = sys.exc_info()
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40 print(" stack trace: " + str(traceback.format_exception(ty, va, tb)))
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41 # exit(-1)
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42 return None # was handle(e)
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43
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44
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45 def __main__():
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46
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47 DROP_TABLES_SQL = """
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48 DROP VIEW IF EXISTS ppep_gene_site_view;
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49 DROP VIEW IF EXISTS uniprot_view;
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50 DROP VIEW IF EXISTS uniprotkb_pep_ppep_view;
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51 DROP VIEW IF EXISTS ppep_intensity_view;
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52 DROP VIEW IF EXISTS ppep_metadata_view;
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53
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54 DROP TABLE IF EXISTS sample;
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55 DROP TABLE IF EXISTS ppep;
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56 DROP TABLE IF EXISTS site_type;
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57 DROP TABLE IF EXISTS deppep_UniProtKB;
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58 DROP TABLE IF EXISTS deppep;
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59 DROP TABLE IF EXISTS ppep_gene_site;
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60 DROP TABLE IF EXISTS ppep_metadata;
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61 DROP TABLE IF EXISTS ppep_intensity;
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62 """
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63
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64 CREATE_TABLES_SQL = """
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65 CREATE TABLE deppep
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66 ( id INTEGER PRIMARY KEY
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67 , seq TEXT UNIQUE ON CONFLICT IGNORE
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68 )
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69 ;
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70 CREATE TABLE deppep_UniProtKB
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71 ( deppep_id INTEGER REFERENCES deppep(id) ON DELETE CASCADE
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72 , UniProtKB_id TEXT REFERENCES UniProtKB(id) ON DELETE CASCADE
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73 , pos_start INTEGER
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74 , pos_end INTEGER
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75 , PRIMARY KEY (deppep_id, UniProtKB_id, pos_start, pos_end)
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76 ON CONFLICT IGNORE
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77 )
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78 ;
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79 CREATE TABLE ppep
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80 ( id INTEGER PRIMARY KEY
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81 , deppep_id INTEGER REFERENCES deppep(id) ON DELETE CASCADE
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82 , seq TEXT UNIQUE ON CONFLICT IGNORE
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83 , scrubbed TEXT
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84 );
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85 CREATE TABLE site_type
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86 ( id INTEGER PRIMARY KEY
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
87 , type_name TEXT UNIQUE ON CONFLICT IGNORE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
88 );
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
89 CREATE INDEX idx_ppep_scrubbed on ppep(scrubbed)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
90 ;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
91 CREATE TABLE sample
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
92 ( id INTEGER PRIMARY KEY
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
93 , name TEXT UNIQUE ON CONFLICT IGNORE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
94 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
95 ;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
96 CREATE VIEW uniprot_view AS
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
97 SELECT DISTINCT
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
98 Uniprot_ID
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
99 , Description
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
100 , Organism_Name
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
101 , Organism_ID
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
102 , Gene_Name
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
103 , PE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
104 , SV
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
105 , Sequence
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
106 , Description ||
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
107 CASE WHEN Organism_Name = 'N/A'
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
108 THEN ''
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
109 ELSE ' OS='|| Organism_Name
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
110 END ||
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
111 CASE WHEN Organism_ID = -1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
112 THEN ''
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
113 ELSE ' OX='|| Organism_ID
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
114 END ||
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
115 CASE WHEN Gene_Name = 'N/A'
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
116 THEN ''
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
117 ELSE ' GN='|| Gene_Name
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
118 END ||
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
119 CASE WHEN PE = 'N/A'
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
120 THEN ''
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
121 ELSE ' PE='|| PE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
122 END ||
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
123 CASE WHEN SV = 'N/A'
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
124 THEN ''
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
125 ELSE ' SV='|| SV
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
126 END AS long_description
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
127 , Database
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
128 FROM UniProtKB
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
129 ;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
130 CREATE VIEW uniprotkb_pep_ppep_view AS
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
131 SELECT deppep_UniProtKB.UniprotKB_ID AS accession
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
132 , deppep_UniProtKB.pos_start AS pos_start
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
133 , deppep_UniProtKB.pos_end AS pos_end
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
134 , deppep.seq AS peptide
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
135 , ppep.seq AS phosphopeptide
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
136 , ppep.scrubbed AS scrubbed
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
137 , uniprot_view.Sequence AS sequence
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
138 , uniprot_view.Description AS description
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
139 , uniprot_view.long_description AS long_description
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
140 , ppep.id AS ppep_id
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
141 FROM ppep, deppep, deppep_UniProtKB, uniprot_view
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
142 WHERE deppep.id = ppep.deppep_id
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
143 AND deppep.id = deppep_UniProtKB.deppep_id
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
144 AND deppep_UniProtKB.UniprotKB_ID = uniprot_view.Uniprot_ID
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
145 ORDER BY UniprotKB_ID, deppep.seq, ppep.seq
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
146 ;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
147 CREATE TABLE ppep_gene_site
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
148 ( ppep_id INTEGER REFERENCES ppep(id)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
149 , gene_names TEXT
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
150 , site_type_id INTEGER REFERENCES site_type(id)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
151 , kinase_map TEXT
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
152 , PRIMARY KEY (ppep_id, kinase_map) ON CONFLICT IGNORE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
153 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
154 ;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
155 CREATE VIEW ppep_gene_site_view AS
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
156 SELECT DISTINCT
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
157 ppep.seq AS phospho_peptide
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
158 , ppep_id
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
159 , gene_names
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
160 , type_name
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
161 , kinase_map
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
162 FROM
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
163 ppep, ppep_gene_site, site_type
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
164 WHERE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
165 ppep_gene_site.ppep_id = ppep.id
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
166 AND
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
167 ppep_gene_site.site_type_id = site_type.id
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
168 ORDER BY
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
169 ppep.seq
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
170 ;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
171 CREATE TABLE ppep_metadata
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
172 ( ppep_id INTEGER REFERENCES ppep(id)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
173 , protein_description TEXT
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
174 , gene_name TEXT
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
175 , FASTA_name TEXT
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176 , phospho_sites TEXT
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177 , motifs_unique TEXT
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178 , accessions TEXT
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179 , motifs_all_members TEXT
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180 , domain TEXT
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181 , ON_FUNCTION TEXT
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182 , ON_PROCESS TEXT
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183 , ON_PROT_INTERACT TEXT
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184 , ON_OTHER_INTERACT TEXT
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185 , notes TEXT
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186 , PRIMARY KEY (ppep_id) ON CONFLICT IGNORE
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187 )
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188 ;
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189 CREATE VIEW ppep_metadata_view AS
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190 SELECT DISTINCT
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191 ppep.seq AS phospho_peptide
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192 , protein_description
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193 , gene_name
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194 , FASTA_name
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195 , phospho_sites
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196 , motifs_unique
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197 , accessions
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198 , motifs_all_members
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199 , domain
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200 , ON_FUNCTION
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201 , ON_PROCESS
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202 , ON_PROT_INTERACT
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203 , ON_OTHER_INTERACT
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204 , notes
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205 FROM
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206 ppep, ppep_metadata
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207 WHERE
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208 ppep_metadata.ppep_id = ppep.id
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209 ORDER BY
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210 ppep.seq
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211 ;
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212 CREATE TABLE ppep_intensity
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213 ( ppep_id INTEGER REFERENCES ppep(id)
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214 , sample_id INTEGER
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215 , intensity INTEGER
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216 , PRIMARY KEY (ppep_id, sample_id) ON CONFLICT IGNORE
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217 )
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218 ;
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219 CREATE VIEW ppep_intensity_view AS
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220 SELECT DISTINCT
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221 ppep.seq AS phospho_peptide
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222 , sample.name AS sample
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223 , intensity
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224 FROM
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225 ppep, sample, ppep_intensity
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226 WHERE
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227 ppep_intensity.sample_id = sample.id
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228 AND
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229 ppep_intensity.ppep_id = ppep.id
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230 ;
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231 """
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232
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233 UNIPROT_SEQ_AND_ID_SQL = """
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234 select Sequence, Uniprot_ID
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235 from UniProtKB
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236 """
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237
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238 # Parse Command Line
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239 parser = argparse.ArgumentParser(
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240 description="Phopsphoproteomic Enrichment phosphopeptide SwissProt search (in place in SQLite DB)."
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241 )
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242
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243 # inputs:
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244 # Phosphopeptide data for experimental results, including the intensities
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245 # and the mapping to kinase domains, in tabular format.
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246 parser.add_argument(
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247 "--phosphopeptides",
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248 "-p",
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249 nargs=1,
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250 required=True,
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251 dest="phosphopeptides",
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252 help="Phosphopeptide data for experimental results, generated by the Phopsphoproteomic Enrichment Localization Filter tool",
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253 )
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254 parser.add_argument(
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255 "--uniprotkb",
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256 "-u",
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257 nargs=1,
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258 required=True,
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259 dest="uniprotkb",
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260 help="UniProtKB/Swiss-Prot data, converted from FASTA format by the Phopsphoproteomic Enrichment Kinase Mapping tool",
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261 )
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262 parser.add_argument(
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263 "--schema",
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264 action="store_true",
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265 dest="db_schema",
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266 help="show updated database schema",
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267 )
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268 parser.add_argument(
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269 "--warn-duplicates",
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270 action="store_true",
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271 dest="warn_duplicates",
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272 help="show warnings for duplicated sequences",
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273 )
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274 parser.add_argument(
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275 "--verbose",
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276 action="store_true",
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277 dest="verbose",
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278 help="show somewhat verbose program tracing",
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279 )
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280 # "Make it so!" (parse the arguments)
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281 options = parser.parse_args()
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282 if options.verbose:
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283 print("options: " + str(options) + "\n")
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284
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285 # path to phosphopeptide (e.g., "outputfile_STEP2.txt") input tabular file
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286 if options.phosphopeptides is None:
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287 exit('Argument "phosphopeptides" is required but not supplied')
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288 try:
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289 f_name = os.path.abspath(options.phosphopeptides[0])
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290 except Exception as e:
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291 exit("Error parsing phosphopeptides argument: %s" % (e))
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292
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293 # path to SQLite input/output tabular file
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294 if options.uniprotkb is None:
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295 exit('Argument "uniprotkb" is required but not supplied')
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296 try:
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297 db_name = os.path.abspath(options.uniprotkb[0])
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298 except Exception as e:
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299 exit("Error parsing uniprotkb argument: %s" % (e))
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300
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301 # print("options.schema is %d" % options.db_schema)
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302
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303 # db_name = "demo/test.sqlite"
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304 # f_name = "demo/test_input.txt"
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305
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306 con = sqlite3.connect(db_name)
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307 cur = con.cursor()
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308 ker = con.cursor()
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309
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310 cur.executescript(DROP_TABLES_SQL)
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311
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312 # if options.db_schema:
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313 # print("\nAfter dropping tables/views that are to be created, schema is:")
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314 # cur.execute("SELECT * FROM sqlite_schema")
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315 # for row in cur.fetchall():
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316 # if row[4] is not None:
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317 # print("%s;" % row[4])
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318
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319 cur.executescript(CREATE_TABLES_SQL)
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320
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321 if options.db_schema:
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322 print(
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323 "\nAfter creating tables/views that are to be created, schema is:"
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324 )
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325 cur.execute("SELECT * FROM sqlite_schema")
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326 for row in cur.fetchall():
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327 if row[4] is not None:
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328 print("%s;" % row[4])
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329
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330 def generate_ppep(f):
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331 # get keys from upstream tabular file using readline()
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332 # ref: https://stackoverflow.com/a/16713581/15509512
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333 # answer to "Use codecs to read file with correct encoding"
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334 file1_encoded = open(f, "rb")
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335 file1 = cx_getreader("latin-1")(file1_encoded)
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336
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337 count = 0
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338 re_tab = re.compile("^[^\t]*")
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339 re_quote = re.compile('"')
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340 while True:
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341 count += 1
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342 # Get next line from file
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343 line = file1.readline()
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344 # if line is empty
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345 # end of file is reached
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346 if not line:
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347 break
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348 if count > 1:
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349 m = re_tab.match(line)
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350 m = re_quote.sub("", m[0])
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351 yield m
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352 file1.close()
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353 file1_encoded.close()
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diff changeset
354
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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355 # Build an Aho-Corasick automaton from a trie
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
356 # - ref:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
357 # - https://pypi.org/project/pyahocorasick/
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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358 # - https://en.wikipedia.org/wiki/Aho%E2%80%93Corasick_algorithm
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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359 # - https://en.wikipedia.org/wiki/Trie
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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360 auto = ahocorasick.Automaton()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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361 re_phos = re.compile("p")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
362 # scrub out unsearchable characters per section
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
363 # "Match the p_peptides to the @sequences array:"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
364 # of the original
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
365 # PhosphoPeptide Upstream Kinase Mapping.pl
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
366 # which originally read
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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367 # $tmp_p_peptide =~ s/#//g;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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368 # $tmp_p_peptide =~ s/\d//g;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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369 # $tmp_p_peptide =~ s/\_//g;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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370 # $tmp_p_peptide =~ s/\.//g;
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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371 #
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
372 re_scrub = re.compile("0-9_.#")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
373 ppep_count = 0
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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374 for ppep in generate_ppep(f_name):
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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375 ppep_count += 1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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376 add_to_trie = False
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
377 # print(ppep)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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378 scrubbed = re_scrub.sub("", ppep)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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379 deppep = re_phos.sub("", scrubbed)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
380 if options.verbose:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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381 print("deppep: %s; scrubbed: %s" % (deppep, scrubbed))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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382 # print(deppep)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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383 cur.execute("SELECT id FROM deppep WHERE seq = (?)", (deppep,))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
384 if cur.fetchone() is None:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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385 add_to_trie = True
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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386 cur.execute("INSERT INTO deppep(seq) VALUES (?)", (deppep,))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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387 cur.execute("SELECT id FROM deppep WHERE seq = (?)", (deppep,))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
388 deppep_id = cur.fetchone()[0]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
389 if add_to_trie:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
390 # print((deppep_id, deppep))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
391 # Build the trie
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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392 auto.add_word(deppep, (deppep_id, deppep))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
393 cur.execute(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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394 "INSERT INTO ppep(seq, scrubbed, deppep_id) VALUES (?,?,?)",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
395 (ppep, scrubbed, deppep_id),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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396 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
397 # def generate_deppep():
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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398 # cur.execute("SELECT seq FROM deppep")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
399 # for row in cur.fetchall():
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
400 # yield row[0]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
401 cur.execute("SELECT count(*) FROM (SELECT seq FROM deppep GROUP BY seq)")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
402 for row in cur.fetchall():
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
403 deppep_count = row[0]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
404
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
405 cur.execute(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
406 "SELECT count(*) FROM (SELECT Sequence FROM UniProtKB GROUP BY Sequence)"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
407 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
408 for row in cur.fetchall():
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff changeset
409 sequence_count = row[0]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
410
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
411 print("%d phosphopeptides were read from input" % ppep_count)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
412 print(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
413 "%d corresponding dephosphopeptides are represented in input"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
414 % deppep_count
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
415 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
416 # Look for cases where both Gene_Name and Sequence are identical
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
417 cur.execute(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
418 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
419 SELECT Uniprot_ID, Gene_Name, Sequence
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
420 FROM UniProtKB
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
421 WHERE Sequence IN (
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
422 SELECT Sequence
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
423 FROM UniProtKB
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
424 GROUP BY Sequence, Gene_Name
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
425 HAVING count(*) > 1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
426 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
427 ORDER BY Sequence
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
428 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
429 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
430 duplicate_count = 0
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
431 old_seq = ""
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
432 for row in cur.fetchall():
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
433 if duplicate_count == 0:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
434 print(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
435 "\nEach of the following sequences is associated with several accession IDs (which are listed in the first column) but the same gene ID (which is listed in the second column)."
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
436 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
437 if row[2] != old_seq:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
438 old_seq = row[2]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
439 duplicate_count += 1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
440 if options.warn_duplicates:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff changeset
441 print("\n%s\t%s\t%s" % row)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
442 else:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
443 if options.warn_duplicates:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
444 print("%s\t%s" % (row[0], row[1]))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
445 if duplicate_count > 0:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
446 print(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
447 "\n%d sequences have duplicated accession IDs\n" % duplicate_count
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
448 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
449
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
450 print("%s accession sequences will be searched\n" % sequence_count)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
451
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
452 # print(auto.dump())
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
453
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
454 # Convert the trie to an automaton (a finite-state machine)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
455 auto.make_automaton()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
456
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
457 # Execute query for seqs and metadata without fetching the results yet
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
458 uniprot_seq_and_id = cur.execute(UNIPROT_SEQ_AND_ID_SQL)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
459 while 1:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
460 batch = uniprot_seq_and_id.fetchmany(size=50)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
461 if not batch:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
462 break
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
463 for Sequence, UniProtKB_id in batch:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
464 if Sequence is not None:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
465 for end_index, (insert_order, original_value) in auto.iter(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
466 Sequence
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
467 ):
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
468 ker.execute(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
469 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
470 INSERT INTO deppep_UniProtKB
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
471 (deppep_id,UniProtKB_id,pos_start,pos_end)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
472 VALUES (?,?,?,?)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
473 """,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
474 (
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
475 insert_order,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
476 UniProtKB_id,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
477 1 + end_index - len(original_value),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
478 end_index,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
479 ),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
480 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
481 else:
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
482 raise ValueError(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
483 "UniProtKB_id %s, but Sequence is None: Check whether SwissProt file is missing sequence for this ID"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
484 % (UniProtKB_id,)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
485 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
486 ker.execute(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
487 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
488 SELECT count(*) || ' accession-peptide-phosphopeptide combinations were found'
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
489 FROM uniprotkb_pep_ppep_view
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
490 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
491 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
492 for row in ker.fetchall():
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
493 print(row[0])
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
494
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
495 ker.execute(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
496 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
497 SELECT count(*) || ' accession matches were found', count(*) AS accession_count
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
498 FROM (
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
499 SELECT accession
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
500 FROM uniprotkb_pep_ppep_view
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
501 GROUP BY accession
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
502 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
503 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
504 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
505 for row in ker.fetchall():
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
506 print(row[0])
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
507
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
508 ker.execute(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
509 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
510 SELECT count(*) || ' peptide matches were found'
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
511 FROM (
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
512 SELECT peptide
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
513 FROM uniprotkb_pep_ppep_view
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
514 GROUP BY peptide
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
515 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
516 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
517 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
518 for row in ker.fetchall():
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
519 print(row[0])
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
520
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
521 ker.execute(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
522 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
523 SELECT count(*) || ' phosphopeptide matches were found', count(*) AS phosphopeptide_count
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
524 FROM (
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
525 SELECT phosphopeptide
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
526 FROM uniprotkb_pep_ppep_view
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
527 GROUP BY phosphopeptide
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
528 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
529 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
530 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff changeset
531 for row in ker.fetchall():
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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532 print(row[0])
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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533
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534 # link peptides not found in sequence database to a dummy sequence-record
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535 ker.execute(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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536 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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537 INSERT INTO deppep_UniProtKB(deppep_id,UniProtKB_id,pos_start,pos_end)
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538 SELECT id, 'No Uniprot_ID', 0, 0
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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539 FROM deppep
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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540 WHERE id NOT IN (SELECT deppep_id FROM deppep_UniProtKB)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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541 """
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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542 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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543
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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544 con.commit()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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545 ker.execute("vacuum")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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546 con.close()
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547
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548
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549 if __name__ == "__main__":
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550 wrap_start_time = time.perf_counter()
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551 __main__()
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552 wrap_stop_time = time.perf_counter()
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553 # print(wrap_start_time)
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554 # print(wrap_stop_time)
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555 print(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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556 "\nThe matching process took %d milliseconds to run.\n"
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557 % ((wrap_stop_time - wrap_start_time) * 1000),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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558 )
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559
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560 # vim: sw=4 ts=4 et ai :