comparison 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
comparison
equal deleted inserted replaced
23:66a183c44dd5 24:248b06e86022
4 import subprocess 4 import subprocess
5 from Population import Population 5 from Population import Population
6 6
7 ################################################################################ 7 ################################################################################
8 8
9 if len(sys.argv) < 11: 9 if len(sys.argv) < 12:
10 print >> sys.stderr, "Usage" 10 print >> sys.stderr, "Usage"
11 sys.exit(1) 11 sys.exit(1)
12 12
13 input, p1_input, p2_input, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:10] 13 input, p1_input, p2_input, input_type, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:11]
14 individual_metadata = sys.argv[10:] 14 individual_metadata = sys.argv[11:]
15 15
16 try: 16 try:
17 shuffle_count = int(shuffles) 17 shuffle_count = int(shuffles)
18 except: 18 except:
19 shuffle_count = 0 19 shuffle_count = 0
53 args.append(discard_fixed) 53 args.append(discard_fixed)
54 args.append(shuffles) 54 args.append(shuffles)
55 55
56 columns = p1.column_list() 56 columns = p1.column_list()
57 for column in columns: 57 for column in columns:
58 if input_type == 'gd_genotype':
59 column = int(column) - 2
58 args.append('{0}:1'.format(column)) 60 args.append('{0}:1'.format(column))
59 61
60 columns = p2.column_list() 62 columns = p2.column_list()
61 for column in columns: 63 for column in columns:
64 if input_type == 'gd_genotype':
65 column = int(column) - 2
62 args.append('{0}:2'.format(column)) 66 args.append('{0}:2'.format(column))
63 67
64 if p0 is not None: 68 if p0 is not None:
65 columns = p0.column_list() 69 columns = p0.column_list()
66 for column in columns: 70 for column in columns:
71 if input_type == 'gd_genotype':
72 column = int(column) - 2
67 args.append('{0}:0'.format(column)) 73 args.append('{0}:0'.format(column))
68 74
69 fh = open(output, 'w') 75 fh = open(output, 'w')
70 76
71 #print "args:", ' '.join(args) 77 #print "args:", ' '.join(args)