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comparison dpmix.py @ 24:248b06e86022

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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
comparison
equal deleted inserted replaced
23:66a183c44dd5 24:248b06e86022
39 print >> sys.stderr, stderrdata 39 print >> sys.stderr, stderrdata
40 sys.exit(1) 40 sys.exit(1)
41 41
42 ################################################################################ 42 ################################################################################
43 43
44 if len(sys.argv) < 15: 44 if len(sys.argv) < 16:
45 print "usage" 45 print "usage"
46 sys.exit(1) 46 sys.exit(1)
47 47
48 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] 48 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]
49 individual_metadata = sys.argv[14:] 49 individual_metadata = sys.argv[15:]
50 50
51 chrom = 'all' 51 chrom = 'all'
52 add_logs = '0' 52 add_logs = '0'
53 53
54 loc_path = os.path.join(galaxy_data_index_dir, heterochromatin_loc_file) 54 loc_path = os.path.join(galaxy_data_index_dir, heterochromatin_loc_file)
102 args.append(heterochrom_path) 102 args.append(heterochrom_path)
103 args.append(misc_file) 103 args.append(misc_file)
104 104
105 columns = ap1.column_list() 105 columns = ap1.column_list()
106 for column in columns: 106 for column in columns:
107 args.append('{0}:1:{1}'.format(column, ap1.individual_with_column(column).name)) 107 if input_type == 'gd_genotype':
108 args.append('{0}:1:{1}'.format(int(column) - 2, ap1.individual_with_column(column).name))
109 else:
110 args.append('{0}:1:{1}'.format(column, ap1.individual_with_column(column).name))
108 111
109 columns = ap2.column_list() 112 columns = ap2.column_list()
110 for column in columns: 113 for column in columns:
111 args.append('{0}:2:{1}'.format(column, ap2.individual_with_column(column).name)) 114 if input_type == 'gd_genotype':
115 args.append('{0}:2:{1}'.format(int(column) - 2, ap2.individual_with_column(column).name))
116 else:
117 args.append('{0}:2:{1}'.format(column, ap2.individual_with_column(column).name))
112 118
113 columns = p.column_list() 119 columns = p.column_list()
114 for column in columns: 120 for column in columns:
115 args.append('{0}:0:{1}'.format(column, p.individual_with_column(column).name)) 121 if input_type == 'gd_genotype':
122 args.append('{0}:0:{1}'.format(int(column) - 2, p.individual_with_column(column).name))
123 else:
124 args.append('{0}:0:{1}'.format(column, p.individual_with_column(column).name))
116 125
117 run_program(None, args, stdout_file=output, space_to_tab=True) 126 run_program(None, args, stdout_file=output, space_to_tab=True)
118 127
119 ################################################################################ 128 ################################################################################
120 # Create pdf file 129 # Create pdf file