44 lines
1.2 KiB
Python
Executable File
44 lines
1.2 KiB
Python
Executable File
from farm_commands2 import *
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import os
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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] b36VCF hg18VCF"
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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) != 2:
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parser.error("incorrect number of arguments")
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b36vcf, hg18vcf = args
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temp = open("tmp", 'w')
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mitotemp = open("mtmp",'w')
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for line in open(b36vcf):
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length = len(line)
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if length > 2 and line[0] != '#':
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if line[0:2] == 'MT':
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spline = line.split("\t")
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spline[0] = "chrM"
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mitotemp.write("\t".join(spline))
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line = 'chr' + line
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temp.write(line)
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out.close()
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mitotemp.close()
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os.system("cat mtmp tmp > "+hg18vcf+" ; rm mtmp ; rm tmp")
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if __name__ == "__main__":
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main()
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