Mercurial > repos > miller-lab > genome_diversity

comparison modify_snp_table.py @ 12:4b6590dd7250

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author miller-lab
date Wed, 12 Sep 2012 17:10:26 -0400
parents 2c498d40ecde
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11:d4ec09e8079f 12:4b6590dd7250
1 #!/usr/bin/env python
2
3 import sys
4 import subprocess
5 from Population import Population
6
7 ################################################################################
8
9 if len(sys.argv) < 9:
10 print >> sys.stderr, "Usage"
11 sys.exit(1)
12
13 input, p1_input, output, lo, hi, lo_ind, lo_ind_qual = sys.argv[1:8]
14 individual_metadata = sys.argv[8:]
15
16 p_total = Population()
17 p_total.from_tag_list(individual_metadata)
18
19 p1 = Population()
20 p1.from_population_file(p1_input)
21
22 if not p_total.is_superset(p1):
23 print >> sys.stderr, 'There is an individual in the population that is not in the SNP table'
24 sys.exit(1)
25
26 ################################################################################
27
28 prog = 'pop'
29
30 args = []
31 args.append(prog)
32 args.append(input)
33 args.append(lo)
34 args.append(hi)
35 args.append(lo_ind)
36 args.append(lo_ind_qual)
37
38 columns = p1.column_list()
39
40 for column in sorted(columns):
41 args.append(column)
42
43 fh = open(output, 'w')
44
45 #print "args:", ' '.join(args)
46 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
47 rc = p.wait()
48 fh.close()
49
50 sys.exit(0)
51