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1 #!/usr/bin/python
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2 # python parser module to analyse sRbowtie alignments
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3 # version 1.0.0 - argparse implementation
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4 # Usage sRbowtieParser.py <1:index source> <2:extraction directive> <3:outputL> <4:polarity> <5:6:7 filePath:FileExt:FileLabel> <.. ad lib>
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5
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6 import sys, argparse
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7 from smRtools import *
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8
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9 def Parser():
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10 the_parser = argparse.ArgumentParser()
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11 the_parser.add_argument('--IndexSource', action="store", type=str, help="Path to the index source")
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12 the_parser.add_argument('--ExtractDirective', action="store", type=str, choices=["fastaSource", "bowtieIndex"], help="Extract info from fasta or bowtie index")
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13 the_parser.add_argument('--output', action="store", type=str, help="path to the output")
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14 the_parser.add_argument('--polarity', choices=["forward", "reverse", "both"], help="forward, reverse or both forward an reverse reads are counted")
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15 the_parser.add_argument('--alignmentSource',nargs='+', help="paths to alignments files")
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16 the_parser.add_argument('--alignmentFormat',nargs='+', help="Format of the bowtie alignment (tabular, sam or bam)")
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17 the_parser.add_argument('--alignmentLabel',nargs='+', help="Label of the alignment")
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18 args = the_parser.parse_args()
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19 return args
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20
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21 args = Parser()
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22
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23 IndexSource = args.IndexSource
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24 genomeRefFormat = args.ExtractDirective
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25 Output = args.output
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26 Polarity = args.polarity
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27 MasterListOfGenomes = {}
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28
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29 for filePath, FileExt, FileLabel in zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel):
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30 MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat)
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31
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32 header = ["gene"]
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33 for filePath, FileExt, FileLabel in zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel):
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34 header.append(FileLabel)
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35
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36 F = open (args.output, "w")
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37 # print >>F, args
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38 print >> F, "\t".join(header)
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39 for item in sorted (MasterListOfGenomes[header[1]].instanceDict.keys() ):
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40 line=[item]
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41 for sample in header[1:]:
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42 count = str (MasterListOfGenomes[sample].instanceDict[item].readcount(polarity=Polarity))
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43 line.append(count)
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44 print >> F, "\t".join(line )
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45 F.close()
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