Mercurial > repos > galaxyp > map_peptides_to_bed
annotate map_peptides_to_bed.py @ 1:db90662d26f9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
author | galaxyp |
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date | Mon, 22 Feb 2016 17:30:45 -0500 |
parents | 51f8f9041724 |
children | 704ea6303c4c |
rev | line source |
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51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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1 #!/usr/bin/env python |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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2 """ |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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3 # |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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4 #------------------------------------------------------------------------------ |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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5 # University of Minnesota |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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6 # Copyright 2014, Regents of the University of Minnesota |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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7 #------------------------------------------------------------------------------ |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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8 # Author: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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9 # |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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10 # James E Johnson |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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11 # |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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12 #------------------------------------------------------------------------------ |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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13 """ |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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14 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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15 """ |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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16 Input: list of protein_accessions, peptide_sequence |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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17 GFF3 with fasta |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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18 Output: GFF3 of peptides |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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19 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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20 Filter: Must cross splice boundary |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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21 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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22 """ |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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23 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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24 import sys,re,os.path |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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25 import tempfile |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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26 import optparse |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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27 from optparse import OptionParser |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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28 from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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29 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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30 class BedEntry( object ): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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31 def __init__(self, line): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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32 self.line = line |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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33 try: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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34 fields = line.rstrip('\r\n').split('\t') |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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35 (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts) = fields[0:12] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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36 seq = fields[12] if len(fields) > 12 else None |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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37 self.chrom = chrom |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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38 self.chromStart = int(chromStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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39 self.chromEnd = int(chromEnd) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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40 self.name = name |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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41 self.score = int(score) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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42 self.strand = strand |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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43 self.thickStart = int(thickStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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44 self.thickEnd = int(thickEnd) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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45 self.itemRgb = itemRgb |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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46 self.blockCount = int(blockCount) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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47 self.blockSizes = [int(x) for x in blockSizes.split(',')] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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48 self.blockStarts = [int(x) for x in blockStarts.split(',')] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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49 self.seq = seq |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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50 except Exception, e: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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51 print >> sys.stderr, "Unable to read Bed entry" % e |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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52 exit(1) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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53 def __str__(self): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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54 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' % ( |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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55 self.chrom, self.chromStart, self.chromEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount, |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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56 ','.join([str(x) for x in self.blockSizes]), |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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57 ','.join([str(x) for x in self.blockStarts]), |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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58 '\t%s' % self.seq if self.seq else '') |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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59 def get_splice_junctions(self): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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60 splice_juncs = [] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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61 for i in range(self.blockCount - 1): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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62 splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1]) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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63 splice_juncs.append(splice_junc) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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64 return splice_juncs |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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65 def get_exon_seqs(self): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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66 exons = [] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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67 for i in range(self.blockCount): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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68 # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1]) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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69 exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]]) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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70 if self.strand == '-': #reverse complement |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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71 exons.reverse() |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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72 for i,s in enumerate(exons): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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73 exons[i] = reverse_complement(s) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff
changeset
|
74 return exons |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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diff
changeset
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75 def get_spliced_seq(self): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff
changeset
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76 seq = ''.join(self.get_exon_seqs()) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff
changeset
|
77 return seq |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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78 def get_translation(self,sequence=None): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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79 translation = None |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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80 seq = sequence if sequence else self.get_spliced_seq() |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff
changeset
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81 if seq: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
82 seqlen = len(seq) / 3 * 3; |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff
changeset
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83 if seqlen >= 3: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
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84 translation = translate(seq[:seqlen]) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff
changeset
|
85 return translation |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
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86 def get_translations(self): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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87 translations = [] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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88 seq = self.get_spliced_seq() |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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89 if seq: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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90 for i in range(3): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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91 translation = self.get_translation(sequence=seq[i:]) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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92 if translation: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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93 translations.append(translation) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
|
94 return translations |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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95 ## (start,end) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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96 def get_subrange(self,tstart,tstop): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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97 chromStart = self.chromStart |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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98 chromEnd = self.chromEnd |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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99 r = range(self.blockCount) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
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100 if self.strand == '-': |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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101 r.reverse() |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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102 bStart = 0 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
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103 for x in r: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
104 bEnd = bStart + self.blockSizes[x] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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105 ## print >> sys.stderr, "%d chromStart: %d chromEnd: %s bStart: %s bEnd: %d" % (x,chromStart,chromEnd,bStart,bEnd) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
106 if bStart <= tstart < bEnd: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
|
107 if self.strand == '+': |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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|
108 chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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109 else: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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diff
changeset
|
110 chromEnd = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstart - bStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
111 if bStart <= tstop < bEnd: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff
changeset
|
112 if self.strand == '+': |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff
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|
113 chromEnd = self.chromStart + self.blockStarts[x] + (tstop - bStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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114 else: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
115 chromStart = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstop - bStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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|
116 bStart += self.blockSizes[x] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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117 return(chromStart,chromEnd) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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118 #get the blocks for sub range |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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119 def get_blocks(self,chromStart,chromEnd): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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120 tblockCount = 0 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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121 tblockSizes = [] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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122 tblockStarts = [] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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123 for x in range(self.blockCount): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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124 bStart = self.chromStart + self.blockStarts[x] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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125 bEnd = bStart + self.blockSizes[x] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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126 if bStart > chromEnd: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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|
127 break |
51f8f9041724
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galaxyp
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128 if bEnd < chromStart: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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129 continue |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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130 cStart = max(chromStart,bStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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131 tblockStarts.append(cStart - chromStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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132 tblockSizes.append(min(chromEnd,bEnd) - cStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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133 tblockCount += 1 |
51f8f9041724
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134 print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes) |
51f8f9041724
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galaxyp
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135 return (tblockCount,tblockSizes,tblockStarts) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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|
136 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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137 ## [[start,end,seq,blockCount,blockSizes,blockStarts],[start,end,seq,blockCount,blockSizes,blockStarts],[start,end,seq,blockCount,blockSizes,blockStarts]] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
138 ## filter: ignore translation if stop codon in first exon after ignore_left_bp |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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|
139 def get_filterd_translations(self,untrimmed=False,filtering=True,ignore_left_bp=0,ignore_right_bp=0): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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140 translations = [None,None,None,None,None,None] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
|
141 seq = self.get_spliced_seq() |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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142 ignore = (ignore_left_bp if self.strand == '+' else ignore_right_bp) / 3 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
143 block_sum = sum(self.blockSizes) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
144 exon_sizes = self.blockSizes |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
|
145 if self.strand == '-': |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
|
146 exon_sizes.reverse() |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
|
147 splice_sites = [sum(exon_sizes[:x]) / 3 for x in range(1,len(exon_sizes))] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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148 print >> sys.stderr, "splice_sites: %s" % splice_sites |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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149 junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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150 if seq: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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151 for i in range(3): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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152 translation = self.get_translation(sequence=seq[i:]) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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153 if translation: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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154 tstart = 0 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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155 tstop = len(translation) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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156 if not untrimmed: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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157 tstart = translation.rfind('*',0,junc) + 1 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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158 stop = translation.find('*',junc) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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159 tstop = stop if stop >= 0 else len(translation) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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160 if filtering and tstart > ignore: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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161 continue |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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162 trimmed = translation[tstart:tstop] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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163 #get genomic locations for start and end |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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164 offset = (block_sum - i) % 3 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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165 print >> sys.stderr, "tstart: %d tstop: %d offset: %d" % (tstart,tstop,offset) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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166 if self.strand == '+': |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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167 chromStart = self.chromStart + i + (tstart * 3) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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168 chromEnd = self.chromEnd - offset - (len(translation) - tstop) * 3 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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169 else: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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170 chromStart = self.chromStart + offset + (len(translation) - tstop) * 3 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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171 chromEnd = self.chromEnd - i - (tstart * 3) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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172 #get the blocks for this translation |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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173 tblockCount = 0 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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174 tblockSizes = [] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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175 tblockStarts = [] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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176 for x in range(self.blockCount): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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177 bStart = self.chromStart + self.blockStarts[x] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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178 bEnd = bStart + self.blockSizes[x] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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179 if bStart > chromEnd: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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|
180 break |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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181 if bEnd < chromStart: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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182 continue |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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183 cStart = max(chromStart,bStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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184 tblockStarts.append(cStart - chromStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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185 tblockSizes.append(min(chromEnd,bEnd) - cStart) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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186 tblockCount += 1 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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187 print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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188 translations[i] = [chromStart,chromEnd,trimmed,tblockCount,tblockSizes,tblockStarts] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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189 return translations |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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190 def get_seq_id(self,seqtype='unk:unk',reference='',frame=None): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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191 ## Ensembl fasta ID format |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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192 # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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193 # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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194 frame_name = '' |
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195 chromStart = self.chromStart |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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196 chromEnd = self.chromEnd |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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197 strand = 1 if self.strand == '+' else -1 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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198 if frame != None: |
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199 block_sum = sum(self.blockSizes) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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200 offset = (block_sum - frame) % 3 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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201 frame_name = '_' + str(frame + 1) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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202 if self.strand == '+': |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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203 chromStart += frame |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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204 chromEnd -= offset |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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205 else: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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206 chromStart += offset |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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207 chromEnd -= frame |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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208 location = "chromosome:%s:%s:%s:%s:%s" % (reference,self.chrom,chromStart,chromEnd,strand) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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209 seq_id = "%s%s %s %s" % (self.name,frame_name,seqtype,location) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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210 return seq_id |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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211 def get_line(self, start_offset = 0, end_offset = 0): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
212 if start_offset or end_offset: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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213 s_offset = start_offset if start_offset else 0 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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|
214 e_offset = end_offset if end_offset else 0 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff
changeset
|
215 if s_offset > self.chromStart: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
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changeset
|
216 s_offset = self.chromStart |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
217 chrStart = self.chromStart - s_offset |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
|
218 chrEnd = self.chromEnd + e_offset |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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changeset
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219 blkSizes = self.blockSizes |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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|
220 blkSizes[0] += s_offset |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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221 blkSizes[-1] += e_offset |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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222 blkStarts = self.blockStarts |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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223 for i in range(1,self.blockCount): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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224 blkStarts[i] += s_offset |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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225 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])]] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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226 return '\t'.join(items) + '\n' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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227 return self.line |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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228 |
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229 def __main__(): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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230 #Parse Command Line |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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231 parser = optparse.OptionParser() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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232 parser.add_option( '-t', '--translated_bed', dest='translated_bed', default=None, help='A bed file with added 13th column having a translation' ) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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233 parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' ) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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234 parser.add_option( '-p', '--peptide_column', type='int', dest='peptide_column', default=1, help='column ordinal with peptide sequence' ) |
1
db90662d26f9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
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235 parser.add_option( '-n', '--name_column', type='int', dest='name_column', default=2, help='column ordinal with protein name' ) |
0
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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236 parser.add_option( '-s', '--start_column', type='int', dest='start_column', default=None, help='column with peptide start position in protein' ) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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237 parser.add_option( '-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation' ) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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238 ## parser.add_option( '-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file' ) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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239 ## parser.add_option( '-f', '--fasta', dest='fasta', default=None, help='Protein fasta' ) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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240 parser.add_option( '-T', '--gffTags', dest='gffTags', action='store_true', default=False, help='Add #gffTags to bed output for IGV' ) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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241 parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr' ) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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242 (options, args) = parser.parse_args() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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243 # Input files |
51f8f9041724
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244 if options.input != None: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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245 try: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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246 inputPath = os.path.abspath(options.input) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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247 inputFile = open(inputPath, 'r') |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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248 except Exception, e: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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249 print >> sys.stderr, "failed: %s" % e |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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250 exit(2) |
51f8f9041724
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251 else: |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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252 inputFile = sys.stdin |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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253 inputBed = None |
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254 if options.translated_bed != None: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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255 inputBed = open(os.path.abspath(options.translated_bed),'r') |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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256 peptide_column = options.peptide_column - 1 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
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257 name_column = options.name_column - 1 if options.name_column else None |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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258 start_column = options.start_column - 1 if options.start_column else None |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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259 # Read in peptides |
51f8f9041724
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260 # peps[prot_name] = [seq] |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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261 prot_peps = dict() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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262 unassigned_peps = set() |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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263 try: |
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264 for i, line in enumerate( inputFile ): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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265 ## print >> sys.stderr, "%3d\t%s" % (i,line) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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266 if line.startswith('#'): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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267 continue |
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268 fields = line.rstrip('\r\n').split('\t') |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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269 ## print >> sys.stderr, "%3d\t%s" % (i,fields) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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270 if peptide_column < len(fields): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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271 peptide = fields[peptide_column] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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272 prot_name = fields[name_column] if name_column is not None and name_column < len(fields) else None |
51f8f9041724
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273 if prot_name: |
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274 offset = fields[start_column] if start_column is not None and start_column < len(fields) else -1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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275 if prot_name not in prot_peps: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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276 prot_peps[prot_name] = dict() |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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277 prot_peps[prot_name][peptide] = offset |
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278 else: |
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279 unassigned_peps.add(peptide) |
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280 if options.debug: |
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281 print >> sys.stderr, "prot_peps: %s" % prot_peps |
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282 print >> sys.stderr, "unassigned_peps: %s" % unassigned_peps |
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283 except Exception, e: |
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284 print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e) |
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285 exit(1) |
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286 # Output files |
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287 bed_fh = None |
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288 ## gff_fh = None |
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289 ## gff_fa_file = None |
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290 gff_fa = None |
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291 outFile = None |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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292 if options.bed: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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293 bed_fh = open(options.bed,'w') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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294 bed_fh.write('track name="%s" type=bedDetail description="%s" \n' % ('novel_junction_peptides','test')) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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295 if options.gffTags: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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296 bed_fh.write('#gffTags\n') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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297 ## if options.gff: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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298 ## gff_fh = open(options.gff,'w') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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299 ## gff_fh.write("##gff-version 3.2.1\n") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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300 ## if options.reference: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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301 ## gff_fh.write("##genome-build %s %s\n" % (options.refsource if options.refsource else 'unknown', options.reference)) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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302 try: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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303 for i, line in enumerate( inputBed ): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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304 ## print >> sys.stderr, "%3d:\t%s" % (i,line) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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305 if line.startswith('track'): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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306 continue |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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307 entry = BedEntry(line) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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308 if entry.name in prot_peps: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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309 for (peptide,offset) in prot_peps[entry.name].iteritems(): |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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310 if offset < 0: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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311 offset = entry.seq.find(peptide) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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312 if options.debug: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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313 print >> sys.stderr, "%s\t%s\t%d\t%s\n" % (entry.name, peptide,offset,entry.seq) |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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314 if offset >= 0: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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315 tstart = offset * 3 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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316 tstop = tstart + len(peptide) * 3 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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317 if options.debug: |
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318 print >> sys.stderr, "%d\t%d\t%d" % (offset,tstart,tstop) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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319 (pepStart,pepEnd) = entry.get_subrange(tstart,tstop) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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320 if options.debug: |
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321 print >> sys.stderr, "%d\t%d\t%d" % (offset,pepStart,pepEnd) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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322 if bed_fh: |
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323 entry.thickStart = pepStart |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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324 entry.thickEnd = pepEnd |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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325 bedfields = str(entry).split('\t') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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326 if options.gffTags: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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327 bedfields[3] = "ID=%s;Name=%s" % (entry.name,peptide) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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328 bed_fh.write("%s\t%s\t%s\n" % ('\t'.join(bedfields[:12]),peptide,entry.seq)) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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329 except Exception, e: |
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330 print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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331 |
51f8f9041724
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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332 if __name__ == "__main__" : __main__() |
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333 |