# HG changeset patch # User jjohnson # Date 1511207898 18000 # Node ID 4702e7f629bb8c5cc82520ef73e739a5f6b3ae1c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bed_to_protein_map commit 38e8d0e983c3aa314e13bdc9ea98f4a728b7772c-dirty diff -r 000000000000 -r 4702e7f629bb bed_to_protein_map.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_to_protein_map.py Mon Nov 20 14:58:18 2017 -0500 @@ -0,0 +1,120 @@ +#!/usr/bin/env python +""" +""" +import sys +import os.path +import optparse + +""" +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 +grep ENST bed_to_protein_map.py | grep -v grep | ./bed_to_protein_map.py +""" + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + #I/O + parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' ) + parser.add_option( '-c', '--column', type='int', dest='column', default=1, help='column ordinal with Ensembl transcript ID' ) + parser.add_option( '-g', '--gtf', dest='gtf', default=None, help='GTF gene model file. Used to annotate NSJ peptide entries.') + parser.add_option( '-2', '--twobit', dest='twobit', default=None, help='Reference genome in UCSC twobit format') + parser.add_option( '-C', '--coding', dest='coding', action='store_true', default=False, help='Output coding BED line') + parser.add_option( '-o', '--output', dest='output', default=None, help='The output bed (else write to stdout)' ) + parser.add_option( '-s', '--sqlitedb', dest='sqlitedb', default=None, help='The sqlitedb' ) + parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Print debugging messages') + (options, args) = parser.parse_args() + ##INPUTS## + if options.input != None: + try: + inputPath = os.path.abspath(options.input) + inputFile = open(inputPath, 'r') + except Exception, e: + print >> sys.stderr, "failed: %s" % e + exit(2) + else: + inputFile = sys.stdin + + if options.output != None: + try: + outputPath = os.path.abspath(options.output) + outputFile = open(outputPath, 'w') + except Exception, e: + print >> sys.stderr, "failed: %s" % e + exit(3) + else: + outputFile = sys.stdout + + dbFile = None + if options.sqlitedb != None: + try: + dbPath = os.path.abspath(options.sqlitedb) + dbFile = open(dbPath, 'w') + except Exception, e: + print >> sys.stderr, "failed: %s" % e + exit(3) + + + try: + for linenum,line in enumerate(inputFile): + if options.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) + chromEnd = int(_chromEnd) + 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) + ##dbFile.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n' % (name,chrom,start,end,strand,cds_start,cds_end)) + outputFile.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) + outputFile.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__() + diff -r 000000000000 -r 4702e7f629bb bed_to_protein_map.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_to_protein_map.xml Mon Nov 20 14:58:18 2017 -0500 @@ -0,0 +1,70 @@ + + genomic location of proteins for MVP + + + + + + + + + + + + + + + + + + + + + + + = cds_start AND cds_offset < cds_end + + +.. _Query_Tabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/1ea4e668bf73 + + ]]> + diff -r 000000000000 -r 4702e7f629bb test-data/input.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.bed Mon Nov 20 14:58:18 2017 -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 diff -r 000000000000 -r 4702e7f629bb test-data/output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tabular Mon Nov 20 14:58:18 2017 -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