Mercurial > repos > devteam > vcf_intersect
diff vcfPytools.py @ 0:f5d5eed73180 draft default tip
Imported from capsule None
author | devteam |
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date | Thu, 23 Jan 2014 12:31:34 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfPytools.py Thu Jan 23 12:31:34 2014 -0500 @@ -0,0 +1,82 @@ +#!/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()