Mercurial > repos > drosofff > msp_sr_bowtie_parser

comparison sRbowtieParser.py @ 0:3a510730e3fc draft

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Imported from capsule None
author drosofff
date Mon, 03 Nov 2014 10:27:20 -0500
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children 70193ce0540e
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-1:000000000000 0:3a510730e3fc
1 #!/usr/bin/python
2 # python parser module to analyse sRbowtie alignments
3 # version 1.0.0 - argparse implementation
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, argparse
7 from smRtools import *
8
9 def Parser():
10 the_parser = argparse.ArgumentParser()
11 the_parser.add_argument('--IndexSource', action="store", type=str, help="Path to the index source")
12 the_parser.add_argument('--ExtractDirective', action="store", type=str, choices=["fastaSource", "bowtieIndex"], help="Extract info from fasta or bowtie index")
13 the_parser.add_argument('--output', action="store", type=str, help="path to the output")
14 the_parser.add_argument('--polarity', choices=["forward", "reverse", "both"], help="forward, reverse or both forward an reverse reads are counted")
15 the_parser.add_argument('--alignmentSource',nargs='+', help="paths to alignments files")
16 the_parser.add_argument('--alignmentFormat',nargs='+', help="Format of the bowtie alignment (tabular, sam or bam)")
17 the_parser.add_argument('--alignmentLabel',nargs='+', help="Label of the alignment")
18 args = the_parser.parse_args()
19 return args
20
21 args = Parser()
22
23 IndexSource = args.IndexSource
24 genomeRefFormat = args.ExtractDirective
25 Output = args.output
26 Polarity = args.polarity
27 MasterListOfGenomes = {}
28
29 for filePath, FileExt, FileLabel in zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel):
30 MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat)
31
32 header = ["gene"]
33 for filePath, FileExt, FileLabel in zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel):
34 header.append(FileLabel)
35
36 F = open (args.output, "w")
37 # print >>F, args
38 print >> F, "\t".join(header)
39 for item in sorted (MasterListOfGenomes[header[1]].instanceDict.keys() ):
40 line=[item]
41 for sample in header[1:]:
42 count = str (MasterListOfGenomes[sample].instanceDict[item].readcount(polarity=Polarity))
43 line.append(count)
44 print >> F, "\t".join(line )
45 F.close()