Mercurial > repos > miller-lab > genome_diversity
diff dpmix.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 | 4b6590dd7250 |
children | 8997f2ca8c7a |
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--- a/dpmix.py Wed May 22 15:58:18 2013 -0400 +++ b/dpmix.py Tue May 28 16:24:19 2013 -0400 @@ -41,12 +41,12 @@ ################################################################################ -if len(sys.argv) < 15: +if len(sys.argv) < 16: print "usage" sys.exit(1) -input, data_source, switch_penalty, ap1_input, ap2_input, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir, heterochromatin_loc_file = sys.argv[1:14] -individual_metadata = sys.argv[14:] +input, input_type, data_source, switch_penalty, ap1_input, ap2_input, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir, heterochromatin_loc_file = sys.argv[1:15] +individual_metadata = sys.argv[15:] chrom = 'all' add_logs = '0' @@ -104,15 +104,24 @@ columns = ap1.column_list() for column in columns: - args.append('{0}:1:{1}'.format(column, ap1.individual_with_column(column).name)) + if input_type == 'gd_genotype': + args.append('{0}:1:{1}'.format(int(column) - 2, ap1.individual_with_column(column).name)) + else: + args.append('{0}:1:{1}'.format(column, ap1.individual_with_column(column).name)) columns = ap2.column_list() for column in columns: - args.append('{0}:2:{1}'.format(column, ap2.individual_with_column(column).name)) + if input_type == 'gd_genotype': + args.append('{0}:2:{1}'.format(int(column) - 2, ap2.individual_with_column(column).name)) + else: + args.append('{0}:2:{1}'.format(column, ap2.individual_with_column(column).name)) columns = p.column_list() for column in columns: - args.append('{0}:0:{1}'.format(column, p.individual_with_column(column).name)) + if input_type == 'gd_genotype': + args.append('{0}:0:{1}'.format(int(column) - 2, p.individual_with_column(column).name)) + else: + args.append('{0}:0:{1}'.format(column, p.individual_with_column(column).name)) run_program(None, args, stdout_file=output, space_to_tab=True)