Mercurial > repos > bgruening > rnaz_annotate

annotate AnnotateRNAz.py @ 0:8c250234fe1d draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author bgruening
date Wed, 30 Jan 2019 03:57:11 -0500
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8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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1 # AnnotateRnaz.py ---
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2 #
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3 # Filename: AnnotateRnaz.py
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4 # Description:
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5 # Author: Joerg Fallmann
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6 # Maintainer:
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7 # Created: Sat Jan 26 12:45:25 2019 (+0100)
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8 # Version:
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9 # Package-Requires: ()
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10 # Last-Updated: Tue Jan 29 13:52:57 2019 (+0100)
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11 # By: Joerg Fallmann
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12 # Update #: 188
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13 # URL:
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14 # Doc URL:
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15 # Keywords:
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16 # Compatibility:
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17 #
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18 #
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19
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20 # Commentary:
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21 # This script is a replacement for rnazAnnotate.pl
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22 # rnazAnnotate can not handle the output from version 2 adequatly
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23 # This script uses the bedtools API to fast intersect an annotation Bed
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24 # with output from RNAz
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25
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26 # Change Log:
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27 #
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28 #
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29 #
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30 #
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31 # This program is free software: you can redistribute it and/or modify
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32 # it under the terms of the GNU General Public License as published by
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33 # the Free Software Foundation, either version 3 of the License, or (at
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34 # your option) any later version.
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35 #
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36 # This program is distributed in the hope that it will be useful, but
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37 # WITHOUT ANY WARRANTY; without even the implied warranty of
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38 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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39 # General Public License for more details.
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40 #
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41 # You should have received a copy of the GNU General Public License
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42 # along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
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43 #
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44 #
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45
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46 # Code:
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47
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48 #!/usr/bin/env python3
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49
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50 import sys
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51 import glob
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52 import argparse
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53 from io import StringIO
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54 import gzip
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55 import traceback as tb
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56 import pybedtools
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57 import re
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58 import tempfile
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59
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60 def parseargs():
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61 parser = argparse.ArgumentParser(description='Intersect RNAz output with Annotation from BED')
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62 parser.add_argument("-b", "--bed", type=str, help='Annotation BED file')
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63 parser.add_argument("-i", "--input", type=str, help='RNAz output')
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64 parser.add_argument("-o", "--bedout", type=str, help='Annotation BED output')
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65 parser.add_argument("-r", "--rnazout", type=str, help='Annotation rnaz output')
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66 return parser.parse_args()
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67
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68 def annotate(bed, input, bedout, rnazout):
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69 try:
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71 pybedtools.set_tempdir('.') # Make sure we do not write somewhere we are not supposed to
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72 anno = pybedtools.BedTool(bed)
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73 rnaz=readrnaz(input)
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74 tmpbed = pybedtools.BedTool(rnaztobed(rnaz), from_string=True)
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75
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76 intersection = tmpbed.intersect(anno,wa=True,wb=True,s=True) # intersect strand specific, keep all info on a and b files
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78 bedtornaz(intersection, rnaz, bedout, rnazout)
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79
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80 return 1
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81
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82 except Exception as err:
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83 exc_type, exc_value, exc_tb = sys.exc_info()
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84 tbe = tb.TracebackException(
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85 exc_type, exc_value, exc_tb,
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86 )
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87 print(''.join(tbe.format()),file=sys.stderr)
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
diff changeset
88
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
89 def readin(file):
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
90 try:
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
91 if '.gz' in file:
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
diff changeset
92 f = gzip.open(file,'rt')
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
diff changeset
93 else:
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bgruening
parents:
diff changeset
94 f = open(file,'rt')
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
95 return f
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
diff changeset
96
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
diff changeset
97 except Exception as err:
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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diff changeset
98 exc_type, exc_value, exc_tb = sys.exc_info()
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
diff changeset
99 tbe = tb.TracebackException(
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
diff changeset
100 exc_type, exc_value, exc_tb,
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
101 )
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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diff changeset
102 print(''.join(tbe.format()),file=sys.stderr)
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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diff changeset
103
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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diff changeset
104 def readrnaz(rnaz):
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parents:
diff changeset
105 try:
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parents:
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106 toparse = readin(rnaz)
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107 tointersect = {}
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108 header = []
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109 for line in toparse:
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110 if '#' in line[0]:
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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111 tointersect['header']=line.strip()
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112 line = re.sub('^#','',line)
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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113 cont = line.strip().split('\t')
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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114 foi = cont.index('seqID') # need to find which column contains seqID
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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115 sf = cont.index('start') # need to find which column contains start
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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116 ef = cont.index('end') # need to find which column contains end
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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117 if 'strand' in cont:# need to find which column contains strand
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parents:
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118 df = cont.index('strand')
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119 else:
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120 df = None
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121 else:
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122 content = line.strip().split('\t')
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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123 newid=re.split('\.|\,|\s|\\|\/|\_', content[foi])[1] # I can only hope that we have species.chromosome.whatever as annotation in aln or maf, if not this is hardly parseable
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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124 if df:
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125 longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', content[df]])
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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126 tointersect[longid] = content
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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127 else:
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128 longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', '+'])
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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129 tointersect[longid] = content
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130 longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', '-'])
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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131 tointersect[longid] = content
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132
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133 return tointersect
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134
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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135 except Exception as err:
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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136 exc_type, exc_value, exc_tb = sys.exc_info()
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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137 tbe = tb.TracebackException(
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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diff changeset
138 exc_type, exc_value, exc_tb,
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139 )
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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140 print(''.join(tbe.format()),file=sys.stderr)
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141
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142
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143 def rnaztobed(rnaz):
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diff changeset
144 try:
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145 tmpbed = []
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diff changeset
146 for key in rnaz:
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147 if key != 'header':
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148 tmpbed.append('\t'.join(key.split('_')))
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149
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150 return '\n'.join(tmpbed)
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151
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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152 except Exception as err:
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153 exc_type, exc_value, exc_tb = sys.exc_info()
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154 tbe = tb.TracebackException(
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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diff changeset
155 exc_type, exc_value, exc_tb,
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156 )
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157 print(''.join(tbe.format()),file=sys.stderr)
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158
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159 def bedtornaz(bed, rnaz, bedout, rnazout):
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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160 try:
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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161 b = open(bedout,'w')
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162 r = open(rnazout,'w')
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diff changeset
163
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parents:
diff changeset
164 annotatedbed=[]
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165 annotatedrnaz=[]
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parents:
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166 annotatedrnaz.append(str.join('\t',[rnaz['header'],'Annotation']))
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
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167 for line in open(bed.fn):
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
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168 out = line.strip().split("\t")
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
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169 annotatedbed.append(str.join('\t',out[0:3]+out[9:10]+out[4:6]))
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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parents:
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170 key = str.join('_',out[0:6])
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parents:
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171 annotatedrnaz.append(str.join('\t',rnaz[key]+out[9:10]))
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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172
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173 print(str.join('\n', annotatedbed),file=b)
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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174 print(str.join('\n', annotatedrnaz),file=r)
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175
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176 except Exception as err:
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177 exc_type, exc_value, exc_tb = sys.exc_info()
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178 tbe = tb.TracebackException(
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179 exc_type, exc_value, exc_tb,
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180 )
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181 print(''.join(tbe.format()),file=sys.stderr)
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182
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183
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184 def closefile(file):
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185 try:
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186 file.close()
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187
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188 except Exception as err:
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189 exc_type, exc_value, exc_tb = sys.exc_info()
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190 tbe = tb.TracebackException(
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191 exc_type, exc_value, exc_tb,
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192 )
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193 print(''.join(tbe.format()),file=sys.stderr)
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194
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195
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196
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197
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198 ####################
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199 #### MAIN ####
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200 ####################
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201 if __name__ == '__main__':
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202 args=parseargs()
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203 annotate(args.bed, args.input, args.bedout, args.rnazout)
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204 ######################################################################
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205 # AnnotateRnaz.py ends here