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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 0.9
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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
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7 from smRtools import *
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8
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9 IndexSource = sys.argv[1]
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10 ExtractionDirective = sys.argv[2]
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11 if ExtractionDirective == "--do_not_extract_index":
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12 genomeRefFormat = "fastaSource"
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13 elif ExtractionDirective == "--extract_index":
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14 genomeRefFormat = "bowtieIndex"
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15 Output = sys.argv[3]
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16 Polarity = sys.argv[4] # maybe "both", "forward", "reverse"
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17 Triplets = [sys.argv[5:][i:i+3] for i in xrange(0, len(sys.argv[5:]), 3)]
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18 MasterListOfGenomes = {}
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19
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20 for [filePath, FileExt, FileLabel] in Triplets:
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21 MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat)
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22
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23 header = ["gene"]
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24 for [filePath, FileExt, FileLabel] in Triplets:
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25 header.append(FileLabel)
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26
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27 F = open (sys.argv[3], "w")
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28 print >> F, "\t".join(header)
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29 for item in sorted (MasterListOfGenomes[header[1]].instanceDict.keys() ):
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30 line=[item]
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31 for sample in header[1:]:
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32 count = str (MasterListOfGenomes[sample].instanceDict[item].readcount(polarity=Polarity))
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33 line.append(count)
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34 print >> F, "\t".join(line )
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35 F.close()
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