39 lines
1.4 KiB
Python
39 lines
1.4 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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if __name__ == "__main__":
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usage = "usage: %prog files.list [options]"
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parser = OptionParser(usage=usage)
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parser.add_option("-f", "--f", dest="fields",
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type='string', default="",
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help="Comma separated list of fields to exact")
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parser.add_option("-e", "--filter", dest="filter",
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action='store_true', default=False,
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help="If true, only includes records that aren't filtered in the output")
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parser.add_option("-s", "--s", dest="skip",
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type='int', default=0,
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help="Only print out every 1 / skip records")
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(OPTIONS, args) = parser.parse_args()
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if len(args) != 0:
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parser.error("incorrect number of arguments")
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counter = OPTIONS.skip
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fields = OPTIONS.fields.split(',')
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for vcf,count in lines2VCF(sys.stdin):
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#print vcf, count
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if count == 1 and vcf.hasHeader():
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print '\t'.join(fields)
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if counter > 0:
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counter -= 1
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else:
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counter = OPTIONS.skip
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if OPTIONS.filter and vcf.failsFilters():
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pass
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else:
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print '\t'.join([ str(vcf.getField(field, '0')) for field in fields])
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