Mercurial > repos > galaxyp > map_peptides_to_bed

annotate map_peptides_to_bed.py @ 4:88d2c4c2cb0a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
author galaxyp
date Mon, 22 Feb 2016 17:31:34 -0500
parents c770d523bd28
children aac354f8d5e8
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c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
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1 #!/usr/bin/env python
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2 """
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3 #
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4 #------------------------------------------------------------------------------
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5 # University of Minnesota
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6 # Copyright 2014, Regents of the University of Minnesota
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7 #------------------------------------------------------------------------------
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8 # Author:
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9 #
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10 # James E Johnson
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11 #
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12 #------------------------------------------------------------------------------
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13 """
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14
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15 """
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16 Input: list of protein_accessions, peptide_sequence
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17 GFF3 with fasta
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18 Output: GFF3 of peptides
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19
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20 Filter: Must cross splice boundary
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21
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22 """
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23
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24 import sys,re,os.path
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25 import tempfile
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26 import optparse
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27 from optparse import OptionParser
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28 from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate
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29
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30 class BedEntry( object ):
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31 def __init__(self, line):
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32 self.line = line
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33 try:
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34 fields = line.rstrip('\r\n').split('\t')
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
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35 (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts) = fields[0:12]
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36 seq = fields[12] if len(fields) > 12 else None
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37 self.chrom = chrom
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38 self.chromStart = int(chromStart)
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39 self.chromEnd = int(chromEnd)
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40 self.name = name
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41 self.score = int(score)
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42 self.strand = strand
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43 self.thickStart = int(thickStart)
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44 self.thickEnd = int(thickEnd)
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45 self.itemRgb = itemRgb
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46 self.blockCount = int(blockCount)
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47 self.blockSizes = [int(x) for x in blockSizes.split(',')]
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48 self.blockStarts = [int(x) for x in blockStarts.split(',')]
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49 self.seq = seq
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50 except Exception, e:
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51 print >> sys.stderr, "Unable to read Bed entry" % e
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52 exit(1)
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53 def __str__(self):
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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' % (
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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,
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56 ','.join([str(x) for x in self.blockSizes]),
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57 ','.join([str(x) for x in self.blockStarts]),
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58 '\t%s' % self.seq if self.seq else '')
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59 def get_splice_junctions(self):
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60 splice_juncs = []
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61 for i in range(self.blockCount - 1):
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62 splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
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63 splice_juncs.append(splice_junc)
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64 return splice_juncs
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65 def get_exon_seqs(self):
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66 exons = []
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67 for i in range(self.blockCount):
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68 # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
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69 exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]])
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70 if self.strand == '-': #reverse complement
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71 exons.reverse()
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72 for i,s in enumerate(exons):
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73 exons[i] = reverse_complement(s)
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74 return exons
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75 def get_spliced_seq(self):
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76 seq = ''.join(self.get_exon_seqs())
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77 return seq
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78 def get_translation(self,sequence=None):
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79 translation = None
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80 seq = sequence if sequence else self.get_spliced_seq()
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81 if seq:
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82 seqlen = len(seq) / 3 * 3;
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83 if seqlen >= 3:
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84 translation = translate(seq[:seqlen])
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85 return translation
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86 def get_translations(self):
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87 translations = []
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88 seq = self.get_spliced_seq()
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89 if seq:
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90 for i in range(3):
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91 translation = self.get_translation(sequence=seq[i:])
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
92 if translation:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
93 translations.append(translation)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
94 return translations
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
95 ## (start,end)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
96 def get_subrange(self,tstart,tstop):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
97 chromStart = self.chromStart
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
98 chromEnd = self.chromEnd
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
99 r = range(self.blockCount)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
100 if self.strand == '-':
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
101 r.reverse()
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
102 bStart = 0
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
103 for x in r:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
104 bEnd = bStart + self.blockSizes[x]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
105 ## print >> sys.stderr, "%d chromStart: %d chromEnd: %s bStart: %s bEnd: %d" % (x,chromStart,chromEnd,bStart,bEnd)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
106 if bStart <= tstart < bEnd:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
107 if self.strand == '+':
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
108 chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
109 else:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
110 chromEnd = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstart - bStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
111 if bStart <= tstop < bEnd:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
112 if self.strand == '+':
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
113 chromEnd = self.chromStart + self.blockStarts[x] + (tstop - bStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
114 else:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
115 chromStart = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstop - bStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
116 bStart += self.blockSizes[x]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
117 return(chromStart,chromEnd)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
118 #get the blocks for sub range
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
119 def get_blocks(self,chromStart,chromEnd):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
120 tblockCount = 0
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
121 tblockSizes = []
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
122 tblockStarts = []
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
123 for x in range(self.blockCount):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
124 bStart = self.chromStart + self.blockStarts[x]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
125 bEnd = bStart + self.blockSizes[x]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
126 if bStart > chromEnd:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
127 break
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
128 if bEnd < chromStart:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
129 continue
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
130 cStart = max(chromStart,bStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
131 tblockStarts.append(cStart - chromStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
132 tblockSizes.append(min(chromEnd,bEnd) - cStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
133 tblockCount += 1
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
134 print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
135 return (tblockCount,tblockSizes,tblockStarts)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
136
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
137 ## [[start,end,seq,blockCount,blockSizes,blockStarts],[start,end,seq,blockCount,blockSizes,blockStarts],[start,end,seq,blockCount,blockSizes,blockStarts]]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
138 ## filter: ignore translation if stop codon in first exon after ignore_left_bp
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
139 def get_filterd_translations(self,untrimmed=False,filtering=True,ignore_left_bp=0,ignore_right_bp=0):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
140 translations = [None,None,None,None,None,None]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
141 seq = self.get_spliced_seq()
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
142 ignore = (ignore_left_bp if self.strand == '+' else ignore_right_bp) / 3
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
143 block_sum = sum(self.blockSizes)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
144 exon_sizes = self.blockSizes
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
145 if self.strand == '-':
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
146 exon_sizes.reverse()
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
147 splice_sites = [sum(exon_sizes[:x]) / 3 for x in range(1,len(exon_sizes))]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
148 print >> sys.stderr, "splice_sites: %s" % splice_sites
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
149 junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
150 if seq:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
151 for i in range(3):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
152 translation = self.get_translation(sequence=seq[i:])
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
153 if translation:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
154 tstart = 0
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
155 tstop = len(translation)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
156 if not untrimmed:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
157 tstart = translation.rfind('*',0,junc) + 1
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
158 stop = translation.find('*',junc)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
159 tstop = stop if stop >= 0 else len(translation)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
160 if filtering and tstart > ignore:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
161 continue
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
162 trimmed = translation[tstart:tstop]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
163 #get genomic locations for start and end
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
164 offset = (block_sum - i) % 3
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
165 print >> sys.stderr, "tstart: %d tstop: %d offset: %d" % (tstart,tstop,offset)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
166 if self.strand == '+':
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
167 chromStart = self.chromStart + i + (tstart * 3)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
168 chromEnd = self.chromEnd - offset - (len(translation) - tstop) * 3
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
169 else:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
170 chromStart = self.chromStart + offset + (len(translation) - tstop) * 3
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
171 chromEnd = self.chromEnd - i - (tstart * 3)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
172 #get the blocks for this translation
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
173 tblockCount = 0
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
174 tblockSizes = []
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
175 tblockStarts = []
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
176 for x in range(self.blockCount):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
177 bStart = self.chromStart + self.blockStarts[x]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
178 bEnd = bStart + self.blockSizes[x]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
179 if bStart > chromEnd:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
180 break
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
181 if bEnd < chromStart:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
182 continue
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
183 cStart = max(chromStart,bStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
184 tblockStarts.append(cStart - chromStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
185 tblockSizes.append(min(chromEnd,bEnd) - cStart)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
186 tblockCount += 1
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
187 print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
188 translations[i] = [chromStart,chromEnd,trimmed,tblockCount,tblockSizes,tblockStarts]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
189 return translations
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
190 def get_seq_id(self,seqtype='unk:unk',reference='',frame=None):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
191 ## Ensembl fasta ID format
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
192 # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
193 # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
194 frame_name = ''
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
195 chromStart = self.chromStart
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
196 chromEnd = self.chromEnd
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
197 strand = 1 if self.strand == '+' else -1
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
198 if frame != None:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
199 block_sum = sum(self.blockSizes)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
200 offset = (block_sum - frame) % 3
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
201 frame_name = '_' + str(frame + 1)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
202 if self.strand == '+':
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
203 chromStart += frame
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
204 chromEnd -= offset
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
205 else:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
206 chromStart += offset
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
207 chromEnd -= frame
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
208 location = "chromosome:%s:%s:%s:%s:%s" % (reference,self.chrom,chromStart,chromEnd,strand)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
209 seq_id = "%s%s %s %s" % (self.name,frame_name,seqtype,location)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
210 return seq_id
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
211 def get_line(self, start_offset = 0, end_offset = 0):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
212 if start_offset or end_offset:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
213 s_offset = start_offset if start_offset else 0
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
214 e_offset = end_offset if end_offset else 0
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
215 if s_offset > self.chromStart:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
216 s_offset = self.chromStart
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
217 chrStart = self.chromStart - s_offset
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
218 chrEnd = self.chromEnd + e_offset
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
219 blkSizes = self.blockSizes
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
220 blkSizes[0] += s_offset
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
221 blkSizes[-1] += e_offset
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
222 blkStarts = self.blockStarts
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
223 for i in range(1,self.blockCount):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
224 blkStarts[i] += s_offset
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
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])]]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
226 return '\t'.join(items) + '\n'
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
227 return self.line
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
228
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
229 def __main__():
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
230 #Parse Command Line
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
231 parser = optparse.OptionParser()
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
232 parser.add_option( '-t', '--translated_bed', dest='translated_bed', default=None, help='A bed file with added 13th column having a translation' )
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
233 parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' )
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
234 parser.add_option( '-p', '--peptide_column', type='int', dest='peptide_column', default=1, help='column ordinal with peptide sequence' )
4
88d2c4c2cb0a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit a2d6625c1d0c65af83ce12614022f30ccd610444-dirty
galaxyp
parents: 0
diff changeset
235 parser.add_option( '-n', '--name_column', type='int', dest='name_column', default=2, help='column ordinal with protein name' )
0
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
236 parser.add_option( '-s', '--start_column', type='int', dest='start_column', default=None, help='column with peptide start position in protein' )
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
237 parser.add_option( '-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation' )
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
238 ## parser.add_option( '-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file' )
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
239 ## parser.add_option( '-f', '--fasta', dest='fasta', default=None, help='Protein fasta' )
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
240 parser.add_option( '-T', '--gffTags', dest='gffTags', action='store_true', default=False, help='Add #gffTags to bed output for IGV' )
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
241 parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr' )
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
242 (options, args) = parser.parse_args()
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
243 # Input files
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
244 if options.input != None:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
245 try:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
246 inputPath = os.path.abspath(options.input)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
247 inputFile = open(inputPath, 'r')
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
248 except Exception, e:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
249 print >> sys.stderr, "failed: %s" % e
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
250 exit(2)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
251 else:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
252 inputFile = sys.stdin
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
253 inputBed = None
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
254 if options.translated_bed != None:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
255 inputBed = open(os.path.abspath(options.translated_bed),'r')
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
256 peptide_column = options.peptide_column - 1
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
257 name_column = options.name_column - 1 if options.name_column else None
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
258 start_column = options.start_column - 1 if options.start_column else None
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
259 # Read in peptides
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
260 # peps[prot_name] = [seq]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
261 prot_peps = dict()
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
262 unassigned_peps = set()
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
263 try:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
264 for i, line in enumerate( inputFile ):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
265 ## print >> sys.stderr, "%3d\t%s" % (i,line)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
266 if line.startswith('#'):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
267 continue
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
268 fields = line.rstrip('\r\n').split('\t')
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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269 ## print >> sys.stderr, "%3d\t%s" % (i,fields)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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270 if peptide_column < len(fields):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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271 peptide = fields[peptide_column]
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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272 prot_name = fields[name_column] if name_column is not None and name_column < len(fields) else None
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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273 if prot_name:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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274 offset = fields[start_column] if start_column is not None and start_column < len(fields) else -1
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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275 if prot_name not in prot_peps:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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276 prot_peps[prot_name] = dict()
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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277 prot_peps[prot_name][peptide] = offset
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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278 else:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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279 unassigned_peps.add(peptide)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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280 if options.debug:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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281 print >> sys.stderr, "prot_peps: %s" % prot_peps
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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282 print >> sys.stderr, "unassigned_peps: %s" % unassigned_peps
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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283 except Exception, e:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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284 print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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285 exit(1)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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286 # Output files
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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287 bed_fh = None
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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288 ## gff_fh = None
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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289 ## gff_fa_file = None
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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290 gff_fa = None
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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291 outFile = None
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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292 if options.bed:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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293 bed_fh = open(options.bed,'w')
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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294 bed_fh.write('track name="%s" type=bedDetail description="%s" \n' % ('novel_junction_peptides','test'))
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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295 if options.gffTags:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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296 bed_fh.write('#gffTags\n')
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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297 ## if options.gff:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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298 ## gff_fh = open(options.gff,'w')
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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299 ## gff_fh.write("##gff-version 3.2.1\n")
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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300 ## if options.reference:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
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301 ## gff_fh.write("##genome-build %s %s\n" % (options.refsource if options.refsource else 'unknown', options.reference))
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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302 try:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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303 for i, line in enumerate( inputBed ):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
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304 ## print >> sys.stderr, "%3d:\t%s" % (i,line)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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305 if line.startswith('track'):
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
306 continue
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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307 entry = BedEntry(line)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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308 if entry.name in prot_peps:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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309 for (peptide,offset) in prot_peps[entry.name].iteritems():
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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310 if offset < 0:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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311 offset = entry.seq.find(peptide)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
312 if options.debug:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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313 print >> sys.stderr, "%s\t%s\t%d\t%s\n" % (entry.name, peptide,offset,entry.seq)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
314 if offset >= 0:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
315 tstart = offset * 3
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
316 tstop = tstart + len(peptide) * 3
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
317 if options.debug:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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318 print >> sys.stderr, "%d\t%d\t%d" % (offset,tstart,tstop)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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319 (pepStart,pepEnd) = entry.get_subrange(tstart,tstop)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
320 if options.debug:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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321 print >> sys.stderr, "%d\t%d\t%d" % (offset,pepStart,pepEnd)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
322 if bed_fh:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
323 entry.thickStart = pepStart
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
324 entry.thickEnd = pepEnd
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
325 bedfields = str(entry).split('\t')
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
326 if options.gffTags:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
327 bedfields[3] = "ID=%s;Name=%s" % (entry.name,peptide)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
328 bed_fh.write("%s\t%s\t%s\n" % ('\t'.join(bedfields[:12]),peptide,entry.seq))
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
329 except Exception, e:
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
330 print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e)
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
331
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
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332 if __name__ == "__main__" : __main__()
c770d523bd28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
galaxyp
parents:
diff changeset
333