Mercurial > repos > devteam > vcf_intersect
view vcfPytools.py @ 0:f5d5eed73180 draft default tip
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author | devteam |
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date | Thu, 23 Jan 2014 12:31:34 -0500 |
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#!/usr/bin/python import os.path import sys __author__ = "alistair ward" __version__ = "version 0.26" __date__ = "february 2011" def main(): usage = "Usage: vcfPytools.py [tool] [options]\n\n" + \ "Available tools:\n" + \ " annotate:\n\tAnnotate the vcf file with membership in other vcf files.\n" + \ " extract:\n\tExtract vcf records from a region.\n" + \ " filter:\n\tFilter the vcf file.\n" + \ " intersect:\n\tGenerate the intersection of two vcf files.\n" + \ " merge:\n\tMerge a list of vcf files.\n" + \ " multi:\n\tFind the intersections and unique fractions of multiple vcf files.\n" + \ " sort:\n\tSort a vcf file.\n" + \ " stats:\n\tGenerate statistics from a vcf file.\n" + \ " union:\n\tGenerate the union of two vcf files.\n" + \ " unique:\n\tGenerate the unique fraction from two vcf files.\n" + \ " validate:\n\tValidate the input vcf file.\n\n" + \ "vcfPytools.py [tool] --help for information on a specific tool." # Determine the requested tool. if len(sys.argv) > 1: tool = sys.argv[1] else: print >> sys.stderr, usage exit(1) if tool == "annotate": import annotate success = annotate.main() elif tool == "extract": import extract success = extract.main() elif tool == "filter": import filter success = filter.main() elif tool == "intersect": import intersect success = intersect.main() elif tool == "multi": import multi success = multi.main() elif tool == "merge": import merge success = merge.main() elif tool == "sort": import sort success = sort.main() elif tool == "stats": import stats success = stats.main() elif tool == "union": import union success = union.main() elif tool == "unique": import unique success = unique.main() elif tool == "test": import test success = test.main() elif tool == "validate": import validate success = validate.main() elif tool == "--help" or tool == "-h" or tool == "?": print >> sys.stderr, usage else: print >> sys.stderr, "Unknown tool: ",tool print >> sys.stderr, "\n", usage exit(1) # If program completed properly, terminate. if success == 0: exit(0) if __name__ == "__main__": main()