# HG changeset patch
# User galaxyp
# Date 1453753969 18000
# Node ID 51f8f9041724c5e6564496e0877eadd9eec23ef6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
diff -r 000000000000 -r 51f8f9041724 map_peptides_to_bed.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/map_peptides_to_bed.py Mon Jan 25 15:32:49 2016 -0500
@@ -0,0 +1,333 @@
+#!/usr/bin/env python
+"""
+#
+#------------------------------------------------------------------------------
+# University of Minnesota
+# Copyright 2014, Regents of the University of Minnesota
+#------------------------------------------------------------------------------
+# Author:
+#
+# James E Johnson
+#
+#------------------------------------------------------------------------------
+"""
+
+"""
+Input: list of protein_accessions, peptide_sequence
+ GFF3 with fasta
+Output: GFF3 of peptides
+
+Filter: Must cross splice boundary
+
+"""
+
+import sys,re,os.path
+import tempfile
+import optparse
+from optparse import OptionParser
+from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate
+
+class BedEntry( object ):
+ def __init__(self, line):
+ self.line = line
+ try:
+ fields = line.rstrip('\r\n').split('\t')
+ (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts) = fields[0:12]
+ seq = fields[12] if len(fields) > 12 else None
+ self.chrom = chrom
+ self.chromStart = int(chromStart)
+ self.chromEnd = int(chromEnd)
+ self.name = name
+ self.score = int(score)
+ self.strand = strand
+ self.thickStart = int(thickStart)
+ self.thickEnd = int(thickEnd)
+ self.itemRgb = itemRgb
+ self.blockCount = int(blockCount)
+ self.blockSizes = [int(x) for x in blockSizes.split(',')]
+ self.blockStarts = [int(x) for x in blockStarts.split(',')]
+ self.seq = seq
+ except Exception, e:
+ print >> sys.stderr, "Unable to read Bed entry" % e
+ exit(1)
+ def __str__(self):
+ return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s%s' % (
+ self.chrom, self.chromStart, self.chromEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount,
+ ','.join([str(x) for x in self.blockSizes]),
+ ','.join([str(x) for x in self.blockStarts]),
+ '\t%s' % self.seq if self.seq else '')
+ def get_splice_junctions(self):
+ splice_juncs = []
+ for i in range(self.blockCount - 1):
+ splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
+ splice_juncs.append(splice_junc)
+ return splice_juncs
+ def get_exon_seqs(self):
+ exons = []
+ for i in range(self.blockCount):
+ # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
+ exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]])
+ if self.strand == '-': #reverse complement
+ exons.reverse()
+ for i,s in enumerate(exons):
+ exons[i] = reverse_complement(s)
+ return exons
+ def get_spliced_seq(self):
+ seq = ''.join(self.get_exon_seqs())
+ return seq
+ def get_translation(self,sequence=None):
+ translation = None
+ seq = sequence if sequence else self.get_spliced_seq()
+ if seq:
+ seqlen = len(seq) / 3 * 3;
+ if seqlen >= 3:
+ translation = translate(seq[:seqlen])
+ return translation
+ def get_translations(self):
+ translations = []
+ seq = self.get_spliced_seq()
+ if seq:
+ for i in range(3):
+ translation = self.get_translation(sequence=seq[i:])
+ if translation:
+ translations.append(translation)
+ return translations
+ ## (start,end)
+ def get_subrange(self,tstart,tstop):
+ chromStart = self.chromStart
+ chromEnd = self.chromEnd
+ r = range(self.blockCount)
+ if self.strand == '-':
+ r.reverse()
+ bStart = 0
+ for x in r:
+ bEnd = bStart + self.blockSizes[x]
+ ## print >> sys.stderr, "%d chromStart: %d chromEnd: %s bStart: %s bEnd: %d" % (x,chromStart,chromEnd,bStart,bEnd)
+ if bStart <= tstart < bEnd:
+ if self.strand == '+':
+ chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart)
+ else:
+ chromEnd = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstart - bStart)
+ if bStart <= tstop < bEnd:
+ if self.strand == '+':
+ chromEnd = self.chromStart + self.blockStarts[x] + (tstop - bStart)
+ else:
+ chromStart = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstop - bStart)
+ bStart += self.blockSizes[x]
+ return(chromStart,chromEnd)
+ #get the blocks for sub range
+ def get_blocks(self,chromStart,chromEnd):
+ tblockCount = 0
+ tblockSizes = []
+ tblockStarts = []
+ for x in range(self.blockCount):
+ bStart = self.chromStart + self.blockStarts[x]
+ bEnd = bStart + self.blockSizes[x]
+ if bStart > chromEnd:
+ break
+ if bEnd < chromStart:
+ continue
+ cStart = max(chromStart,bStart)
+ tblockStarts.append(cStart - chromStart)
+ tblockSizes.append(min(chromEnd,bEnd) - cStart)
+ tblockCount += 1
+ print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes)
+ return (tblockCount,tblockSizes,tblockStarts)
+
+ ## [[start,end,seq,blockCount,blockSizes,blockStarts],[start,end,seq,blockCount,blockSizes,blockStarts],[start,end,seq,blockCount,blockSizes,blockStarts]]
+ ## filter: ignore translation if stop codon in first exon after ignore_left_bp
+ def get_filterd_translations(self,untrimmed=False,filtering=True,ignore_left_bp=0,ignore_right_bp=0):
+ translations = [None,None,None,None,None,None]
+ seq = self.get_spliced_seq()
+ ignore = (ignore_left_bp if self.strand == '+' else ignore_right_bp) / 3
+ block_sum = sum(self.blockSizes)
+ exon_sizes = self.blockSizes
+ if self.strand == '-':
+ exon_sizes.reverse()
+ splice_sites = [sum(exon_sizes[:x]) / 3 for x in range(1,len(exon_sizes))]
+ print >> sys.stderr, "splice_sites: %s" % splice_sites
+ junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0]
+ if seq:
+ for i in range(3):
+ translation = self.get_translation(sequence=seq[i:])
+ if translation:
+ tstart = 0
+ tstop = len(translation)
+ if not untrimmed:
+ tstart = translation.rfind('*',0,junc) + 1
+ stop = translation.find('*',junc)
+ tstop = stop if stop >= 0 else len(translation)
+ if filtering and tstart > ignore:
+ continue
+ trimmed = translation[tstart:tstop]
+ #get genomic locations for start and end
+ offset = (block_sum - i) % 3
+ print >> sys.stderr, "tstart: %d tstop: %d offset: %d" % (tstart,tstop,offset)
+ if self.strand == '+':
+ chromStart = self.chromStart + i + (tstart * 3)
+ chromEnd = self.chromEnd - offset - (len(translation) - tstop) * 3
+ else:
+ chromStart = self.chromStart + offset + (len(translation) - tstop) * 3
+ chromEnd = self.chromEnd - i - (tstart * 3)
+ #get the blocks for this translation
+ tblockCount = 0
+ tblockSizes = []
+ tblockStarts = []
+ for x in range(self.blockCount):
+ bStart = self.chromStart + self.blockStarts[x]
+ bEnd = bStart + self.blockSizes[x]
+ if bStart > chromEnd:
+ break
+ if bEnd < chromStart:
+ continue
+ cStart = max(chromStart,bStart)
+ tblockStarts.append(cStart - chromStart)
+ tblockSizes.append(min(chromEnd,bEnd) - cStart)
+ tblockCount += 1
+ print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes)
+ translations[i] = [chromStart,chromEnd,trimmed,tblockCount,tblockSizes,tblockStarts]
+ return translations
+ def get_seq_id(self,seqtype='unk:unk',reference='',frame=None):
+ ## Ensembl fasta ID format
+ # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT
+ # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding
+ frame_name = ''
+ chromStart = self.chromStart
+ chromEnd = self.chromEnd
+ strand = 1 if self.strand == '+' else -1
+ if frame != None:
+ block_sum = sum(self.blockSizes)
+ offset = (block_sum - frame) % 3
+ frame_name = '_' + str(frame + 1)
+ if self.strand == '+':
+ chromStart += frame
+ chromEnd -= offset
+ else:
+ chromStart += offset
+ chromEnd -= frame
+ location = "chromosome:%s:%s:%s:%s:%s" % (reference,self.chrom,chromStart,chromEnd,strand)
+ seq_id = "%s%s %s %s" % (self.name,frame_name,seqtype,location)
+ return seq_id
+ def get_line(self, start_offset = 0, end_offset = 0):
+ if start_offset or end_offset:
+ s_offset = start_offset if start_offset else 0
+ e_offset = end_offset if end_offset else 0
+ if s_offset > self.chromStart:
+ s_offset = self.chromStart
+ chrStart = self.chromStart - s_offset
+ chrEnd = self.chromEnd + e_offset
+ blkSizes = self.blockSizes
+ blkSizes[0] += s_offset
+ blkSizes[-1] += e_offset
+ blkStarts = self.blockStarts
+ for i in range(1,self.blockCount):
+ blkStarts[i] += s_offset
+ items = [str(x) for x in [self.chrom,chrStart,chrEnd,self.name,self.score,self.strand,self.thickStart,self.thickEnd,self.itemRgb,self.blockCount,','.join([str(x) for x in blkSizes]),','.join([str(x) for x in blkStarts])]]
+ return '\t'.join(items) + '\n'
+ return self.line
+
+def __main__():
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ parser.add_option( '-t', '--translated_bed', dest='translated_bed', default=None, help='A bed file with added 13th column having a translation' )
+ parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' )
+ parser.add_option( '-p', '--peptide_column', type='int', dest='peptide_column', default=1, help='column ordinal with peptide sequence' )
+ parser.add_option( '-n', '--name_column', type='int', dest='name_column', default=None, help='column ordinal with protein name' )
+ parser.add_option( '-s', '--start_column', type='int', dest='start_column', default=None, help='column with peptide start position in protein' )
+ parser.add_option( '-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation' )
+ ## parser.add_option( '-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file' )
+ ## parser.add_option( '-f', '--fasta', dest='fasta', default=None, help='Protein fasta' )
+ parser.add_option( '-T', '--gffTags', dest='gffTags', action='store_true', default=False, help='Add #gffTags to bed output for IGV' )
+ parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr' )
+ (options, args) = parser.parse_args()
+ # Input files
+ 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
+ inputBed = None
+ if options.translated_bed != None:
+ inputBed = open(os.path.abspath(options.translated_bed),'r')
+ peptide_column = options.peptide_column - 1
+ name_column = options.name_column - 1 if options.name_column else None
+ start_column = options.start_column - 1 if options.start_column else None
+ # Read in peptides
+ # peps[prot_name] = [seq]
+ prot_peps = dict()
+ unassigned_peps = set()
+ try:
+ for i, line in enumerate( inputFile ):
+ ## print >> sys.stderr, "%3d\t%s" % (i,line)
+ if line.startswith('#'):
+ continue
+ fields = line.rstrip('\r\n').split('\t')
+ ## print >> sys.stderr, "%3d\t%s" % (i,fields)
+ if peptide_column < len(fields):
+ peptide = fields[peptide_column]
+ prot_name = fields[name_column] if name_column is not None and name_column < len(fields) else None
+ if prot_name:
+ offset = fields[start_column] if start_column is not None and start_column < len(fields) else -1
+ if prot_name not in prot_peps:
+ prot_peps[prot_name] = dict()
+ prot_peps[prot_name][peptide] = offset
+ else:
+ unassigned_peps.add(peptide)
+ if options.debug:
+ print >> sys.stderr, "prot_peps: %s" % prot_peps
+ print >> sys.stderr, "unassigned_peps: %s" % unassigned_peps
+ except Exception, e:
+ print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e)
+ exit(1)
+ # Output files
+ bed_fh = None
+ ## gff_fh = None
+ ## gff_fa_file = None
+ gff_fa = None
+ outFile = None
+ if options.bed:
+ bed_fh = open(options.bed,'w')
+ bed_fh.write('track name="%s" type=bedDetail description="%s" \n' % ('novel_junction_peptides','test'))
+ if options.gffTags:
+ bed_fh.write('#gffTags\n')
+ ## if options.gff:
+ ## gff_fh = open(options.gff,'w')
+ ## gff_fh.write("##gff-version 3.2.1\n")
+ ## if options.reference:
+ ## gff_fh.write("##genome-build %s %s\n" % (options.refsource if options.refsource else 'unknown', options.reference))
+ try:
+ for i, line in enumerate( inputBed ):
+ ## print >> sys.stderr, "%3d:\t%s" % (i,line)
+ if line.startswith('track'):
+ continue
+ entry = BedEntry(line)
+ if entry.name in prot_peps:
+ for (peptide,offset) in prot_peps[entry.name].iteritems():
+ if offset < 0:
+ offset = entry.seq.find(peptide)
+ if options.debug:
+ print >> sys.stderr, "%s\t%s\t%d\t%s\n" % (entry.name, peptide,offset,entry.seq)
+ if offset >= 0:
+ tstart = offset * 3
+ tstop = tstart + len(peptide) * 3
+ if options.debug:
+ print >> sys.stderr, "%d\t%d\t%d" % (offset,tstart,tstop)
+ (pepStart,pepEnd) = entry.get_subrange(tstart,tstop)
+ if options.debug:
+ print >> sys.stderr, "%d\t%d\t%d" % (offset,pepStart,pepEnd)
+ if bed_fh:
+ entry.thickStart = pepStart
+ entry.thickEnd = pepEnd
+ bedfields = str(entry).split('\t')
+ if options.gffTags:
+ bedfields[3] = "ID=%s;Name=%s" % (entry.name,peptide)
+ bed_fh.write("%s\t%s\t%s\n" % ('\t'.join(bedfields[:12]),peptide,entry.seq))
+ except Exception, e:
+ print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e)
+
+if __name__ == "__main__" : __main__()
+
diff -r 000000000000 -r 51f8f9041724 map_peptides_to_bed.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/map_peptides_to_bed.xml Mon Jan 25 15:32:49 2016 -0500
@@ -0,0 +1,68 @@
+
+
+ biopython
+
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diff -r 000000000000 -r 51f8f9041724 test-data/mapped_peptides.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapped_peptides.bed Mon Jan 25 15:32:49 2016 -0500
@@ -0,0 +1,27 @@
+track name="novel_junction_peptides" type=bedDetail description="test"
+#gffTags
+15 40902460 40907575 ID=JUNC00019210_2;Name=RNGRNKKLEDNYCEIT 1 + 40902484 40907575 255,0,0 2 35,37 0,5078 RNGRNKKLEDNYCEIT SYENSEKVRNGRNKKLEDNYCEIT
+15 40902460 40907575 ID=JUNC00019210_2;Name=SYENSEKVR 1 + 40902460 40902487 255,0,0 2 35,37 0,5078 SYENSEKVR SYENSEKVRNGRNKKLEDNYCEIT
+15 40902461 40907549 ID=JUNC00019210_3;Name=KIVRKSEMEGI 1 + 40902467 40907543 255,0,0 2 34,11 0,5077 KIVRKSEMEGI HMKIVRKSEMEGIRN
+9 17406 18053 ID=JUNC00000003_1;Name=LDPLAGAVTKTHV 1 - 17421 17460 255,0,0 2 73,26 0,621 LDPLAGAVTKTHV APWTSGPCRYKKYVFLDPLAGAVTKTHVMLGAE
+9 17406 18053 ID=JUNC00000003_1;Name=LDPLAGAVTKTHVMLGAE 1 - 17406 17460 255,0,0 2 73,26 0,621 LDPLAGAVTKTHVMLGAE APWTSGPCRYKKYVFLDPLAGAVTKTHVMLGAE
+9 17406 18053 ID=JUNC00000003_1;Name=APWTSGPCRYKKYVF 1 - 17460 18053 255,0,0 2 73,26 0,621 APWTSGPCRYKKYVF APWTSGPCRYKKYVFLDPLAGAVTKTHVMLGAE
+9 17404 18051 ID=JUNC00000003_3;Name=CLPGPPGWCCNKDPCDAGGRD 1 - 17404 17467 255,0,0 2 75,24 0,623 CLPGPPGWCCNKDPCDAGGRD PLDERALQVQEVCLPGPPGWCCNKDPCDAGGRD
+9 17404 18051 ID=JUNC00000003_3;Name=PLDERALQVQEVCLPG 1 - 17455 18051 255,0,0 2 75,24 0,623 PLDERALQVQEVCLPG PLDERALQVQEVCLPGPPGWCCNKDPCDAGGRD
+8 27369376 27370079 ID=JUNC00000874_2;Name=PTSCNPSDMSHGYVTVKGYHKAKATHRGPWLVA 1 + 27369376 27370079 255,0,0 2 51,48 0,655 PTSCNPSDMSHGYVTVKGYHKAKATHRGPWLVA PTSCNPSDMSHGYVTVKGYHKAKATHRGPWLVA
+8 27369376 27370079 ID=JUNC00000874_2;Name=DMSHGYVTVKGYHKA 1 + 27369397 27370046 255,0,0 2 51,48 0,655 DMSHGYVTVKGYHKA PTSCNPSDMSHGYVTVKGYHKAKATHRGPWLVA
+7 148909514 148910831 ID=JUNC00002152_1;Name=DQQDLADRDIPTDPNSGENKSLSSQHMTFCHGS 1 + 148909514 148910831 255,0,0 2 60,39 0,1278 DQQDLADRDIPTDPNSGENKSLSSQHMTFCHGS DQQDLADRDIPTDPNSGENKSLSSQHMTFCHGS
+7 148909514 148910831 ID=JUNC00002152_1;Name=DLADRDIPTDP 1 + 148909523 148909556 255,0,0 2 60,39 0,1278 DLADRDIPTDP DQQDLADRDIPTDPNSGENKSLSSQHMTFCHGS
+7 148909515 148910811 ID=JUNC00002152_2;Name=IWQTEIFPRI 1 + 148909524 148909554 255,0,0 2 59,19 0,1277 IWQTEIFPRI ISRIWQTEIFPRIPIQVRTRVSHLST
+7 148909515 148910811 ID=JUNC00002152_2;Name=IFPRIPIQVRTRVSHL 1 + 148909539 148910805 255,0,0 2 59,19 0,1277 IFPRIPIQVRTRVSHL ISRIWQTEIFPRIPIQVRTRVSHLST
+6 41766614 41767580 ID=JUNC00002625_1;Name=LKDSGGLAVIIERRLGSMSSLT 1 - 41766614 41767580 255,0,0 2 53,13 0,953 LKDSGGLAVIIERRLGSMSSLT LKDSGGLAVIIERRLGSMSSLT
+6 41766614 41767580 ID=JUNC00002625_1;Name=DSGGLAVIIERR 1 - 41766638 41767574 255,0,0 2 53,13 0,953 DSGGLAVIIERR LKDSGGLAVIIERRLGSMSSLT
+6 41766614 41767580 ID=JUNC00002625_1;Name=GLAVIIERRLGSMSS 1 - 41766620 41766665 255,0,0 2 53,13 0,953 GLAVIIERRLGSMSS LKDSGGLAVIIERRLGSMSSLT
+6 41766612 41767578 ID=JUNC00002625_3;Name=KRFRWSGRNHREKIGVHVVFDQ 1 - 41766612 41767578 255,0,0 2 55,11 0,955 KRFRWSGRNHREKIGVHVVFDQ KRFRWSGRNHREKIGVHVVFDQ
+6 41766612 41767578 ID=JUNC00002625_3;Name=FRWSGR 1 - 41766654 41767572 255,0,0 2 55,11 0,955 FRWSGR KRFRWSGRNHREKIGVHVVFDQ
+6 41766612 41767578 ID=JUNC00002625_3;Name=NHREKIGVHVVFD 1 - 41766615 41766654 255,0,0 2 55,11 0,955 NHREKIGVHVVFD KRFRWSGRNHREKIGVHVVFDQ
+6 84856497 84862316 ID=JUNC00002772_1;Name=LKMKSEAVMNQFENSMRRYL 1 - 84856497 84862316 255,0,0 2 7,53 0,5766 LKMKSEAVMNQFENSMRRYL LKMKSEAVMNQFENSMRRYL
+6 84856497 84862316 ID=JUNC00002772_1;Name=MNQFENSMRRYL 1 - 84856497 84862292 255,0,0 2 7,53 0,5766 MNQFENSMRRYL LKMKSEAVMNQFENSMRRYL
+6 84856497 84862316 ID=JUNC00002772_1;Name=LKMKSEAVMNQFEN 1 - 84862274 84862316 255,0,0 2 7,53 0,5766 LKMKSEAVMNQFEN LKMKSEAVMNQFENSMRRYL
+6 84856497 84862316 ID=JUNC00002772_1;Name=LKMKSEAV 1 - 84862292 84862316 255,0,0 2 7,53 0,5766 LKMKSEAV LKMKSEAVMNQFENSMRRYL
+6 84856497 84862316 ID=JUNC00002772_1;Name=KSEAVMNQFENSMR 1 - 84862265 84862307 255,0,0 2 7,53 0,5766 KSEAVMNQFENSMR LKMKSEAVMNQFENSMRRYL
diff -r 000000000000 -r 51f8f9041724 test-data/peptides.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptides.tsv Mon Jan 25 15:32:49 2016 -0500
@@ -0,0 +1,25 @@
+JUNC00019210_2 RNGRNKKLEDNYCEIT
+JUNC00019210_2 SYENSEKVR
+JUNC00019210_3 KIVRKSEMEGI
+JUNC00000003_1 LDPLAGAVTKTHVMLGAE
+JUNC00000003_1 APWTSGPCRYKKYVF
+JUNC00000003_1 LDPLAGAVTKTHV
+JUNC00000003_3 PLDERALQVQEVCLPG
+JUNC00000003_3 CLPGPPGWCCNKDPCDAGGRD
+JUNC00000874_2 PTSCNPSDMSHGYVTVKGYHKAKATHRGPWLVA
+JUNC00000874_2 DMSHGYVTVKGYHKA
+JUNC00002152_1 DQQDLADRDIPTDPNSGENKSLSSQHMTFCHGS
+JUNC00002152_1 DLADRDIPTDP
+JUNC00002152_2 IWQTEIFPRI
+JUNC00002152_2 IFPRIPIQVRTRVSHL
+JUNC00002625_1 LKDSGGLAVIIERRLGSMSSLT
+JUNC00002625_1 GLAVIIERRLGSMSS
+JUNC00002625_1 DSGGLAVIIERR
+JUNC00002625_3 FRWSGR
+JUNC00002625_3 KRFRWSGRNHREKIGVHVVFDQ
+JUNC00002625_3 NHREKIGVHVVFD
+JUNC00002772_1 LKMKSEAVMNQFENSMRRYL
+JUNC00002772_1 LKMKSEAVMNQFEN
+JUNC00002772_1 LKMKSEAV
+JUNC00002772_1 MNQFENSMRRYL
+JUNC00002772_1 KSEAVMNQFENSMR
diff -r 000000000000 -r 51f8f9041724 test-data/translated_bed_sequences.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/translated_bed_sequences.bed Mon Jan 25 15:32:49 2016 -0500
@@ -0,0 +1,14 @@
+track name="novel_junctioni_translations" description="test"
+15 40902460 40907575 JUNC00019210_2 1 + 40902460 40907575 255,0,0 2 35,37 0,5078 SYENSEKVRNGRNKKLEDNYCEIT
+15 40902461 40907549 JUNC00019210_3 1 + 40902461 40907549 255,0,0 2 34,11 0,5077 HMKIVRKSEMEGIRN
+9 17406 18053 JUNC00000003_1 1 - 17406 18053 255,0,0 2 73,26 0,621 APWTSGPCRYKKYVFLDPLAGAVTKTHVMLGAE
+9 17438 18052 JUNC00000003_2 1 - 17438 18052 255,0,0 2 41,25 0,589 PPGRAGPAGTRSMSSWTPWLVL
+9 17404 18051 JUNC00000003_3 1 - 17404 18051 255,0,0 2 75,24 0,623 PLDERALQVQEVCLPGPPGWCCNKDPCDAGGRD
+8 27369376 27370079 JUNC00000874_2 1 + 27369376 27370079 255,0,0 2 51,48 0,655 PTSCNPSDMSHGYVTVKGYHKAKATHRGPWLVA
+7 99077597 99079392 JUNC00001897_1 1 + 99077597 99079392 255,0,0 2 64,35 0,1760 HLLSLFFQLGVHICIPNFRNNSVSHCTQLRVLL
+7 99077598 99079360 JUNC00001897_2 1 + 99077598 99079360 255,0,0 2 63,3 0,1759 IYCLYFSNLVCISVYPTSEITV
+7 148909514 148910831 JUNC00002152_1 1 + 148909514 148910831 255,0,0 2 60,39 0,1278 DQQDLADRDIPTDPNSGENKSLSSQHMTFCHGS
+7 148909515 148910811 JUNC00002152_2 1 + 148909515 148910811 255,0,0 2 59,19 0,1277 ISRIWQTEIFPRIPIQVRTRVSHLST
+6 41766614 41767580 JUNC00002625_1 1 - 41766614 41767580 255,0,0 2 53,13 0,953 LKDSGGLAVIIERRLGSMSSLT
+6 41766612 41767578 JUNC00002625_3 1 - 41766612 41767578 255,0,0 2 55,11 0,955 KRFRWSGRNHREKIGVHVVFDQ
+6 84856497 84862316 JUNC00002772_1 1 - 84856497 84862316 255,0,0 2 7,53 0,5766 LKMKSEAVMNQFENSMRRYL
diff -r 000000000000 -r 51f8f9041724 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Jan 25 15:32:49 2016 -0500
@@ -0,0 +1,6 @@
+
+
+
+
+
+