diff filter_vcf.py @ 0:834a312c0114 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_vcf.py	Thu Dec 10 09:22:39 2015 -0500
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+'''Simple VCF parser using custom filters.
+
+Created on 6 Oct 2015
+
+@author: alex
+'''
+import argparse
+
+from phe.variant import VariantSet
+
+
+def get_args():
+
+    args = argparse.ArgumentParser()
+
+    args.add_argument("--vcf", "-v", required=True, help="VCF file to (re)filter.")
+    args.add_argument("--filters", "-f", required=True, help="Filter(s) to apply as key:threshold pairs, separated by comma.")
+    args.add_argument("--output", "-o", required=True, help="Location for filtered VCF to be written.")
+
+    return args.parse_args()
+
+
+def main():
+    args = get_args()
+
+    var_set = VariantSet(args.vcf, filters=args.filters)
+
+    var_set.filter_variants()
+
+    var_set.serialise(args.output)
+
+if __name__ == '__main__':
+    exit(main())