Mercurial > repos > miller-lab > genome_diversity
comparison modify_snp_table.py @ 12:4b6590dd7250
Uploaded
author | miller-lab |
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date | Wed, 12 Sep 2012 17:10:26 -0400 |
parents | 2c498d40ecde |
children |
comparison
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11:d4ec09e8079f | 12:4b6590dd7250 |
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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 |