56 lines
1.6 KiB
Python
56 lines
1.6 KiB
Python
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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 vcfReader import *
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from itertools import *
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import faiReader
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def main():
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global OPTIONS
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usage = "usage: %prog [options] file1 ... fileN"
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parser = OptionParser(usage=usage)
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parser.add_option("-f", "--f", dest="fai",
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type='string', default=None,
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help="FAI file defining the sort order of the VCF")
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(OPTIONS, args) = parser.parse_args()
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if len(args) == 0:
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parser.error("Requires at least 1 VCF to merge")
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order = None
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if OPTIONS.fai <> None: order = faiReader.readFAIContigOrdering(OPTIONS.fai)
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#print 'Order', order
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header = None
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records = []
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for file in args:
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#print file
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for header, record, counter in lines2VCF(open(file), extendedOutput = True, decodeAll = False):
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records.append(record)
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def cmpVCFRecords(r1, r2):
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if order <> None:
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c1 = order[str(r1.getChrom())]
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c2 = order[str(r2.getChrom())]
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orderCmp = cmp(c1, c2)
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if orderCmp <> 0:
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return orderCmp
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return cmp(r1.getPos(), r2.getPos())
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records.sort(cmpVCFRecords)
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for line in formatVCF(header, records):
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#pass
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print line
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PROFILE = False
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if __name__ == "__main__":
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if PROFILE:
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import cProfile
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cProfile.run('main()', 'fooprof')
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import pstats
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p = pstats.Stats('fooprof')
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p.sort_stats('cumulative').print_stats(10)
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p.sort_stats('time').print_stats(10)
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p.sort_stats('time', 'cum').print_stats(.5, 'init')
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else:
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main()
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