40 lines
1.2 KiB
Python
Executable File
40 lines
1.2 KiB
Python
Executable File
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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def main():
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global OPTIONS
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usage = "usage: %prog [options] indelCalls.bed maskSize indelsMask.bed"
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parser = OptionParser(usage=usage)
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#parser.add_option("", "--dry", dest="dry",
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# action='store_true', default=False,
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# help="If provided, nothing actually gets run, just a dry run")
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(OPTIONS, args) = parser.parse_args()
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if len(args) != 3:
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parser.error("incorrect number of arguments")
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indelCalls, maskSize, indelsMask = args
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maskSize = int(maskSize)
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out = open(indelsMask, 'w')
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for line in open(indelCalls):
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# chr1 71996 72005 -AAAAAAAAA:4/6
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chr, indelStart, indelStop, notes = line.split()
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maskStart = int(indelStart) - maskSize
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maskStop = int(indelStop) + maskSize
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maskNotes = notes + ":+/-" + str(maskSize)
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print >> out, '\t'.join([chr, str(maskStart), str(maskStop), maskNotes])
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out.close()
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if __name__ == "__main__":
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main()
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