Mercurial > repos > drosofff > msp_sr_bowtie_parser

annotate sRbowtieParser.py @ 1:ca3845fb0b31 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09
author drosofff
date Mon, 18 Apr 2016 10:09:08 -0400
parents b996480cd604
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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 1.0.2 - 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 masterListGenerator(data_source):
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10 for filePath, FileExt, FileLabel in data_source:
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11 yield HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat)
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12
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13 def Parser():
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14 the_parser = argparse.ArgumentParser()
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15 the_parser.add_argument('--IndexSource', action="store", type=str, help="Path to the index source")
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16 the_parser.add_argument('--ExtractDirective', action="store", type=str, choices=["fastaSource", "bowtieIndex"], help="Extract info from fasta or bowtie index")
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17 the_parser.add_argument('--output', action="store", type=str, help="path to the output")
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18 the_parser.add_argument('--polarity', choices=["forward", "reverse", "both"], help="forward, reverse or both forward an reverse reads are counted")
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19 the_parser.add_argument('--alignmentSource',nargs='+', help="paths to alignments files")
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20 the_parser.add_argument('--alignmentFormat',nargs='+', help="Format of the bowtie alignment (tabular, sam or bam)")
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21 the_parser.add_argument('--alignmentLabel',nargs='+', help="Label of the alignment")
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22 args = the_parser.parse_args()
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23 return args
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24
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25 args = Parser()
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26
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27 IndexSource = args.IndexSource
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28 genomeRefFormat = args.ExtractDirective
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29 Output = args.output
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30 Polarity = args.polarity
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31 header = ["gene"]
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32
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33
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34 FileLabelList=[label for label in args.alignmentLabel]
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35 header.extend(FileLabelList)
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36 assert (len(FileLabelList)==len(set(FileLabelList))),"You have supplied a non-unique label. Please make sure that your input files have unique names"
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37
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38 data_source=zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel)
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39 master_generator=masterListGenerator(data_source)
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40
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41 for i,window in enumerate(master_generator):
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42 window=window
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43 if i==0:
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44 gene_count_dict={gene:[str(item.readcount(polarity=Polarity))] for gene,item in window.instanceDict.items()}
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45 else:
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46 [gene_count_dict[gene].append(str(item.readcount(polarity=Polarity))) for gene,item in window.instanceDict.items()]
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48
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49 F = open (args.output, "w")
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50 # print >>F, args
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51 print >> F, "\t".join(header)
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52
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53 for item in sorted(gene_count_dict.keys()):
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54 line=[item]
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55 line.extend(gene_count_dict[item])
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56 print >> F, "\t".join(line )
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57 F.close()