46 lines
1.5 KiB
Python
46 lines
1.5 KiB
Python
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from farm_commands2 import *
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import os.path
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import sys
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from optparse import OptionParser
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from datetime import date
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import glob
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import operator
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import faiReader
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import math
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import shutil
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import string
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from madPipelineUtils import *
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def main():
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global OPTIONS
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usage = "usage: %prog [options] indels.verbose.txt"
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parser = OptionParser(usage=usage)
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parser.add_option("-v", "--verbose", dest="verbose",
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action='store_true', default=False,
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help="")
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(OPTIONS, args) = parser.parse_args()
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if len(args) != 1:
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parser.error("incorrect number of arguments")
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indelsFile = args[0]
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print 'event size nReadsWithIndel nReadsWithoutIndel nReadsTotal'
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for line in open(indelsFile):
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try:
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parts = line.split()
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# chr1 30502 30505 -TTT OBS_COUNTS[C/A/T]:5/5/13 AV_MM[C/R]:0.00/0.75 AV_MAPQ[C/R]:37.00/27.13 NQS_MM_RATE[C/R]:0.00/0.01 NQS_AV_QUAL[C/R]:30.90/28.30 STRAND_COUNTS[C/C/R/R]:2/3/6/2
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chr, start, stop = parts[0:3]
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event = parts[3]
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counts = parts[4]
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isInsertion = event[0] == '+'
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size = len(event[1:])
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nConsensusReads, nReadsWithIndel, nReads = map(int, counts.split(':')[1].split('/'))
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nReadsWithoutIndel = nReads - nReadsWithIndel
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print event[0], size, nReadsWithIndel, nReadsWithoutIndel, nReads
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except:
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continue
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if __name__ == "__main__":
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main()
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