Mercurial > repos > miller-lab > genome_diversity

comparison add_fst_column.py @ 14:8ae67e9fb6ff

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Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
author miller-lab
date Fri, 28 Sep 2012 11:35:56 -0400
parents 2c498d40ecde
children 248b06e86022
comparison
equal deleted inserted replaced
13:fdb4240fb565 14:8ae67e9fb6ff
1 #!/usr/bin/env python
2
3 # <command interpreter="python">
4 # add_fst_column.py "$input" "$p1_input" "$p2_input" "$data_source.choice" "$data_source.min_value" "$retain" "$discard_fixed" "$biased" "$output"
5 # #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
6 # #set $arg = '%s:%s' % ($individual_col, $individual)
7 # "$arg"
8 # #end for
9 # </command>
10
11 import sys
12 import subprocess
13 from Population import Population
14
15 ################################################################################
16
17 if len(sys.argv) < 12:
18 print >> sys.stderr, "Usage"
19 sys.exit(1)
20
21 input, p1_input, p2_input, genotypes, min_reads, min_qual, retain, discard_fixed, biased, output = sys.argv[1:11]
22 individual_metadata = sys.argv[11:]
23
24 p_total = Population()
25 p_total.from_tag_list(individual_metadata)
26
27 p1 = Population()
28 p1.from_population_file(p1_input)
29 if not p_total.is_superset(p1):
30 print >> sys.stderr, 'There is an individual in population 1 that is not in the SNP table'
31 sys.exit(1)
32
33 p2 = Population()
34 p2.from_population_file(p2_input)
35 if not p_total.is_superset(p2):
36 print >> sys.stderr, 'There is an individual in population 2 that is not in the SNP table'
37 sys.exit(1)
38
39 ################################################################################
40
41 prog = 'Fst_column'
42
43 args = []
44 args.append(prog)
45 args.append(input)
46 args.append(genotypes)
47 args.append(min_reads)
48 args.append(min_qual)
49 args.append(retain)
50 args.append(discard_fixed)
51 args.append(biased)
52
53 columns = p1.column_list()
54 for column in columns:
55 args.append('{0}:1'.format(column))
56
57 columns = p2.column_list()
58 for column in columns:
59 args.append('{0}:2'.format(column))
60
61 fh = open(output, 'w')
62
63 #print "args:", ' '.join(args)
64 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
65 rc = p.wait()
66 fh.close()
67
68 sys.exit(0)
69