annotate modify_snp_table.py @ 0:32f8fbdd754c default tip

Uploaded
author rico
date Fri, 06 Apr 2012 13:59:29 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
32f8fbdd754c Uploaded
rico
parents:
diff changeset
1 #!/usr/bin/env python
32f8fbdd754c Uploaded
rico
parents:
diff changeset
2
32f8fbdd754c Uploaded
rico
parents:
diff changeset
3 import sys
32f8fbdd754c Uploaded
rico
parents:
diff changeset
4 import subprocess
32f8fbdd754c Uploaded
rico
parents:
diff changeset
5 from Population import Population
32f8fbdd754c Uploaded
rico
parents:
diff changeset
6
32f8fbdd754c Uploaded
rico
parents:
diff changeset
7 ################################################################################
32f8fbdd754c Uploaded
rico
parents:
diff changeset
8
32f8fbdd754c Uploaded
rico
parents:
diff changeset
9 if len(sys.argv) < 9:
32f8fbdd754c Uploaded
rico
parents:
diff changeset
10 print >> sys.stderr, "Usage"
32f8fbdd754c Uploaded
rico
parents:
diff changeset
11 sys.exit(1)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
12
32f8fbdd754c Uploaded
rico
parents:
diff changeset
13 input, p1_input, output, lo, hi, lo_ind, lo_ind_qual = sys.argv[1:8]
32f8fbdd754c Uploaded
rico
parents:
diff changeset
14 individual_metadata = sys.argv[8:]
32f8fbdd754c Uploaded
rico
parents:
diff changeset
15
32f8fbdd754c Uploaded
rico
parents:
diff changeset
16 p_total = Population()
32f8fbdd754c Uploaded
rico
parents:
diff changeset
17 p_total.from_tag_list(individual_metadata)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
18
32f8fbdd754c Uploaded
rico
parents:
diff changeset
19 p1 = Population()
32f8fbdd754c Uploaded
rico
parents:
diff changeset
20 p1.from_population_file(p1_input)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
21
32f8fbdd754c Uploaded
rico
parents:
diff changeset
22 if not p_total.is_superset(p1):
32f8fbdd754c Uploaded
rico
parents:
diff changeset
23 print >> sys.stderr, 'There is an individual in the population that is not in the SNP table'
32f8fbdd754c Uploaded
rico
parents:
diff changeset
24 sys.exit(1)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
25
32f8fbdd754c Uploaded
rico
parents:
diff changeset
26 ################################################################################
32f8fbdd754c Uploaded
rico
parents:
diff changeset
27
32f8fbdd754c Uploaded
rico
parents:
diff changeset
28 prog = 'pop'
32f8fbdd754c Uploaded
rico
parents:
diff changeset
29
32f8fbdd754c Uploaded
rico
parents:
diff changeset
30 args = []
32f8fbdd754c Uploaded
rico
parents:
diff changeset
31 args.append(prog)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
32 args.append(input)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
33 args.append(lo)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
34 args.append(hi)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
35 args.append(lo_ind)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
36 args.append(lo_ind_qual)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
37
32f8fbdd754c Uploaded
rico
parents:
diff changeset
38 columns = p1.column_list()
32f8fbdd754c Uploaded
rico
parents:
diff changeset
39
32f8fbdd754c Uploaded
rico
parents:
diff changeset
40 for column in sorted(columns):
32f8fbdd754c Uploaded
rico
parents:
diff changeset
41 args.append(column)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
42
32f8fbdd754c Uploaded
rico
parents:
diff changeset
43 fh = open(output, 'w')
32f8fbdd754c Uploaded
rico
parents:
diff changeset
44
32f8fbdd754c Uploaded
rico
parents:
diff changeset
45 #print "args:", ' '.join(args)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
46 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
47 rc = p.wait()
32f8fbdd754c Uploaded
rico
parents:
diff changeset
48 fh.close()
32f8fbdd754c Uploaded
rico
parents:
diff changeset
49
32f8fbdd754c Uploaded
rico
parents:
diff changeset
50 sys.exit(0)
32f8fbdd754c Uploaded
rico
parents:
diff changeset
51