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comparison aggregate_gd_indivs.py @ 26:91e835060ad2

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Updates to Admixture, Aggregate Individuals, and Restore Attributes to support gd_genotype
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 03 Jun 2013 12:29:29 -0400
parents 95a05c1ef5d5
children 8997f2ca8c7a
comparison
equal deleted inserted replaced
25:cba0d7a63b82 26:91e835060ad2
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) < 9: 9 if len(sys.argv) < 6:
10 print >> sys.stderr, "Usage" 10 print >> sys.stderr, "Usage"
11 sys.exit(1) 11 sys.exit(1)
12 12
13 #input, p1_input, output, lo, hi, lo_ind, lo_ind_qual = sys.argv[1:8] 13 input, p1_input, output, input_type = sys.argv[1:5]
14 #individual_metadata = sys.argv[8:] 14 individual_metadata = sys.argv[5:]
15 input, p1_input, output, = sys.argv[1:4]
16 individual_metadata = sys.argv[4:]
17 15
18 p_total = Population() 16 p_total = Population()
19 p_total.from_tag_list(individual_metadata) 17 p_total.from_tag_list(individual_metadata)
20 18
21 p1 = Population() 19 p1 = Population()
31 29
32 args = [] 30 args = []
33 args.append(prog) 31 args.append(prog)
34 args.append(input) 32 args.append(input)
35 33
34 if input_type == 'gd_snp':
35 args.append('1')
36 elif input_type == 'gd_genotype':
37 args.append('0')
38 else:
39 print >> sys.stderr, "unknown input type:", input_type
40 sys.exit(1)
41
36 columns = p1.column_list() 42 columns = p1.column_list()
37 43
38 for column in sorted(columns): 44 for column in sorted(columns):
45 if input_type == 'gd_genotype':
46 column = str(int(column) - 2)
39 args.append(column) 47 args.append(column)
40 48
41 fh = open(output, 'w') 49 fh = open(output, 'w')
42 50
43 #print "args:", ' '.join(args) 51 #print "args:", ' '.join(args)