50 lines
1.3 KiB
Python
Executable File
50 lines
1.3 KiB
Python
Executable File
import sys
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from optparse import OptionParser
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def getRsIDSet(dbSNPIds, idIndex):
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s = set()
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for line in open(dbSNPIds):
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#print line
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rsID = line.split()[idIndex]
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s.add(rsID)
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return frozenset(s)
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def main():
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global OPTIONS
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usage = "usage: %prog [options] dbSNP.in.rsids dbSNP.to.match dbSNP.out"
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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) != 3:
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parser.error("incorrect number of arguments")
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dbSNPIds = args[0]
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dbSNPMatch = args[1]
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dbSNPOut = args[2]
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idIndex = 4
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rsSet = getRsIDSet(dbSNPIds, idIndex)
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print 'rsID set has %d elements' % len(rsSet)
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#
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count = 0
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matched = 0
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out = open(dbSNPOut, 'w')
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for line in open(dbSNPMatch):
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count += 1
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rsID = line.split()[idIndex]
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if rsID in rsSet:
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#sys.stdout.write(line)
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matched += 1
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out.write(line)
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print 'Processed %d lines, matching %d elements, excluding %d' % ( count, matched, count - matched )
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out.close()
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if __name__ == "__main__":
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main()
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