Mercurial > repos > miller-lab > genome_diversity
diff average_fst.py @ 24:248b06e86022
Added gd_genotype datatype. Modified tools to support new datatype.
author | Richard Burhans <burhans@bx.psu.edu> |
---|---|
date | Tue, 28 May 2013 16:24:19 -0400 |
parents | f04f40a36cc8 |
children | 8997f2ca8c7a |
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--- a/average_fst.py Wed May 22 15:58:18 2013 -0400 +++ b/average_fst.py Tue May 28 16:24:19 2013 -0400 @@ -6,12 +6,12 @@ ################################################################################ -if len(sys.argv) < 11: +if len(sys.argv) < 12: print >> sys.stderr, "Usage" sys.exit(1) -input, p1_input, p2_input, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:10] -individual_metadata = sys.argv[10:] +input, p1_input, p2_input, input_type, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:11] +individual_metadata = sys.argv[11:] try: shuffle_count = int(shuffles) @@ -55,15 +55,21 @@ columns = p1.column_list() for column in columns: + if input_type == 'gd_genotype': + column = int(column) - 2 args.append('{0}:1'.format(column)) columns = p2.column_list() for column in columns: + if input_type == 'gd_genotype': + column = int(column) - 2 args.append('{0}:2'.format(column)) if p0 is not None: columns = p0.column_list() for column in columns: + if input_type == 'gd_genotype': + column = int(column) - 2 args.append('{0}:0'.format(column)) fh = open(output, 'w')