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comparison average_fst.py @ 18:f04f40a36cc8

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Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 23 Oct 2012 12:41:52 -0400
parents 2c498d40ecde
children 248b06e86022
comparison
equal deleted inserted replaced
17:a3af29edcce2 18:f04f40a36cc8
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) < 12: 9 if len(sys.argv) < 11:
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, biased, output, shuffles, p0_input = sys.argv[1:11] 13 input, p1_input, p2_input, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:10]
14 individual_metadata = sys.argv[11:] 14 individual_metadata = sys.argv[10:]
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
49 args.append(prog) 49 args.append(prog)
50 args.append(input) 50 args.append(input)
51 args.append(data_source) 51 args.append(data_source)
52 args.append(min_total_count) 52 args.append(min_total_count)
53 args.append(discard_fixed) 53 args.append(discard_fixed)
54 args.append(biased)
55 args.append(shuffles) 54 args.append(shuffles)
56 55
57 columns = p1.column_list() 56 columns = p1.column_list()
58 for column in columns: 57 for column in columns:
59 args.append('{0}:1'.format(column)) 58 args.append('{0}:1'.format(column))