diff vcfPytools.py @ 0:3eca7b2537aa draft default tip

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfPytools.py	Thu Jan 23 12:31:47 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()