Mercurial > repos > drosofff > parse_srbowtie_alignment

comparison sRbowtieParser.py @ 2:aa7092c7a3c8 draft

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author drosofff
date Mon, 23 Jun 2014 03:57:00 -0400
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1:06e465694fd1 2:aa7092c7a3c8
1 #!/usr/bin/python
2 # python parser module to analyse sRbowtie alignments
3 # version 0.9
4 # Usage sRbowtieParser.py <1:index source> <2:extraction directive> <3:outputL> <4:polarity> <5:6:7 filePath:FileExt:FileLabel> <.. ad lib>
5
6 import sys
7 from smRtools import *
8
9 IndexSource = sys.argv[1]
10 ExtractionDirective = sys.argv[2]
11 if ExtractionDirective == "--do_not_extract_index":
12 genomeRefFormat = "fastaSource"
13 elif ExtractionDirective == "--extract_index":
14 genomeRefFormat = "bowtieIndex"
15 Output = sys.argv[3]
16 Polarity = sys.argv[4] # maybe "both", "forward", "reverse"
17 Triplets = [sys.argv[5:][i:i+3] for i in xrange(0, len(sys.argv[5:]), 3)]
18 MasterListOfGenomes = {}
19
20 for [filePath, FileExt, FileLabel] in Triplets:
21 MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat)
22
23 header = ["gene"]
24 for [filePath, FileExt, FileLabel] in Triplets:
25 header.append(FileLabel)
26
27 F = open (sys.argv[3], "w")
28 print >> F, "\t".join(header)
29 for item in sorted (MasterListOfGenomes[header[1]].instanceDict.keys() ):
30 line=[item]
31 for sample in header[1:]:
32 count = str (MasterListOfGenomes[sample].instanceDict[item].readcount(polarity=Polarity))
33 line.append(count)
34 print >> F, "\t".join(line )
35 F.close()