Mercurial > repos > galaxyp > bed_to_protein_map
changeset 0:7b2642f6c004 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
| author | galaxyp |
|---|---|
| date | Thu, 04 Jan 2018 16:33:42 -0500 |
| parents | |
| children | f270ac79c0a1 |
| files | bed_to_protein_map.py bed_to_protein_map.xml test-data/input.bed test-data/output.tabular |
| diffstat | 4 files changed, 186 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_to_protein_map.py Thu Jan 04 16:33:42 2018 -0500 @@ -0,0 +1,100 @@ +#!/usr/bin/env python +""" +# +#------------------------------------------------------------------------------ +# University of Minnesota +# Copyright 2017, Regents of the University of Minnesota +#------------------------------------------------------------------------------ +# Author: +# +# James E Johnson +# +#------------------------------------------------------------------------------ +""" + +import argparse +import sys + + +def __main__(): + parser = argparse.ArgumentParser( + description='Convert BED file to protein mapping') + parser.add_argument( + 'input', + help='A BED file (12 column)') + parser.add_argument( + 'output', + help='Output file (-) for stdout') + parser.add_argument('-d', '--debug', action='store_true', help='Debug') + args = parser.parse_args() + + input_rdr = open(args.input, 'r') if args.input != '-' else sys.stdin + output_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout + + try: + for linenum, line in enumerate(input_rdr): + if args.debug: + print >> sys.stderr, "%d: %s\n" % (linenum, line) + if line.startswith('#'): + continue + if line.strip() == '': + continue + fields = line.rstrip('\r\n').split('\t') + if len(fields) < 12: + print >> sys.stderr, "%d: %s\n" % (linenum, line) + continue + (chrom, _chromStart, _chromEnd, name, score, strand, + _thickStart, _thickEnd, itemRgb, + _blockCount, blockSizes, blockStarts) = fields[0:12] + chromStart = int(_chromStart) + thickStart = int(_thickStart) + thickEnd = int(_thickEnd) + blockCount = int(_blockCount) + blockSizes = [int(x) for x in blockSizes.split(',')] + blockStarts = [int(x) for x in blockStarts.split(',')] + if strand == '+': + cds_start = 0 + cds_end = 0 + for i in range(blockCount): + start = chromStart + blockStarts[i] + end = start + blockSizes[i] + if end < thickStart: + continue + if start > thickEnd: + break + if start < thickStart: + start = thickStart + if end > thickEnd: + end = thickEnd + cds_end = cds_start + (end - start) + output_wtr.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n' + % (name, chrom, start, end, + strand, cds_start, cds_end)) + cds_start = cds_end + elif strand == '-': + cds_start = 0 + cds_end = 0 + for i in reversed(range(blockCount)): + start = chromStart + blockStarts[i] + end = start + blockSizes[i] + if end < thickStart: + break + if start > thickEnd: + continue + if start < thickStart: + start = thickStart + if end > thickEnd: + end = thickEnd + cds_end = cds_start + (end - start) + output_wtr.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n' + % (name, chrom, start, end, + strand, cds_start, cds_end)) + cds_start = cds_end + pass + except Exception, e: + print >> sys.stderr, "failed: %s" % e + exit(1) + + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_to_protein_map.xml Thu Jan 04 16:33:42 2018 -0500 @@ -0,0 +1,70 @@ +<tool id="bed_to_protein_map" name="bed to protein map" version="0.1.0"> + <description>genomic location of proteins for MVP</description> + <requirements> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python '$__tool_directory__/bed_to_protein_map.py' '$input' '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="bed" label="A BED file with 12 columns, thickStart and thickEnd define protein coding region"/> + </inputs> + <outputs> + <data name="output" format="tabular"> + <actions> + <action name="column_names" type="metadata" default="name,chrom,start,end,strand,cds_start,cds_end"/> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="input" ftype="bed" value="input.bed"/> + <output name="output" file="output.tabular"/> + </test> + </tests> + <help><![CDATA[ +Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP). + +Example input BED dataset:: + + X 276352 291629 ENST00000430923 20 + 284187 291629 80,80,80 5 42,148,137,129,131 0,7814,12380,14295,15146 + X 304749 318819 ENST00000326153 20 - 305073 318787 80,80,80 10 448,153,149,209,159,68,131,71,138,381 0,2610,2982,6669,8016,9400,10140,10479,12164,13689 + + +Output:: + + name chrom start end strand cds_start cds_end + ENST00000430923 X 284187 284314 + 0 127 + ENST00000430923 X 288732 288869 + 127 264 + ENST00000430923 X 290647 290776 + 264 393 + ENST00000430923 X 291498 291629 + 393 524 + ENST00000326153 X 318438 318787 - 0 349 + ENST00000326153 X 316913 317051 - 349 487 + ENST00000326153 X 315228 315299 - 487 558 + ENST00000326153 X 314889 315020 - 558 689 + ENST00000326153 X 314149 314217 - 689 757 + ENST00000326153 X 312765 312924 - 757 916 + ENST00000326153 X 311418 311627 - 916 1125 + ENST00000326153 X 307731 307880 - 1125 1274 + ENST00000326153 X 307359 307512 - 1274 1427 + ENST00000326153 X 305073 305197 - 1427 1551 + + +The tabular output can be converted to a sqlite database using the Query_Tabular_ tool. + +The sqlite table should be named: feature_cds_map +The names for the columns should be: name,chrom,start,end,strand,cds_start,cds_end + +This SQL query will return the genomic location for a peptide sequence in a protein (multiply the animo acid position by 3 for the cds location):: + + SELECT distinct chrom, CASE WHEN strand = '+' THEN start + cds_offset - cds_start ELSE end - cds_offset - cds_start END as "pos" + FROM feature_cds_map + WHERE name = acc_name AND cds_offset >= cds_start AND cds_offset < cds_end + + +.. _Query_Tabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/1ea4e668bf73 + + ]]></help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.bed Thu Jan 04 16:33:42 2018 -0500 @@ -0,0 +1,2 @@ +X 276352 291629 ENST00000430923 20 + 284187 291629 80,80,80 5 42,148,137,129,131 0,7814,12380,14295,15146 +X 304749 318819 ENST00000326153 20 - 305073 318787 80,80,80 10 448,153,149,209,159,68,131,71,138,381 0,2610,2982,6669,8016,9400,10140,10479,12164,13689
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tabular Thu Jan 04 16:33:42 2018 -0500 @@ -0,0 +1,14 @@ +ENST00000430923 X 284187 284314 + 0 127 +ENST00000430923 X 288732 288869 + 127 264 +ENST00000430923 X 290647 290776 + 264 393 +ENST00000430923 X 291498 291629 + 393 524 +ENST00000326153 X 318438 318787 - 0 349 +ENST00000326153 X 316913 317051 - 349 487 +ENST00000326153 X 315228 315299 - 487 558 +ENST00000326153 X 314889 315020 - 558 689 +ENST00000326153 X 314149 314217 - 689 757 +ENST00000326153 X 312765 312924 - 757 916 +ENST00000326153 X 311418 311627 - 916 1125 +ENST00000326153 X 307731 307880 - 1125 1274 +ENST00000326153 X 307359 307512 - 1274 1427 +ENST00000326153 X 305073 305197 - 1427 1551