Mercurial > repos > miller-lab > genome_diversity
comparison add_fst_column.py @ 24:248b06e86022
Added gd_genotype datatype. Modified tools to support new datatype.
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 28 May 2013 16:24:19 -0400 |
| parents | 2c498d40ecde |
| children | 8997f2ca8c7a |
comparison
equal
deleted
inserted
replaced
| 23:66a183c44dd5 | 24:248b06e86022 |
|---|---|
| 16 | 16 |
| 17 if len(sys.argv) < 12: | 17 if len(sys.argv) < 12: |
| 18 print >> sys.stderr, "Usage" | 18 print >> sys.stderr, "Usage" |
| 19 sys.exit(1) | 19 sys.exit(1) |
| 20 | 20 |
| 21 input, p1_input, p2_input, genotypes, min_reads, min_qual, retain, discard_fixed, biased, output = sys.argv[1:11] | 21 input, p1_input, p2_input, input_type, genotypes, min_reads, min_qual, retain, discard_fixed, biased, output = sys.argv[1:12] |
| 22 individual_metadata = sys.argv[11:] | 22 individual_metadata = sys.argv[12:] |
| 23 | 23 |
| 24 p_total = Population() | 24 p_total = Population() |
| 25 p_total.from_tag_list(individual_metadata) | 25 p_total.from_tag_list(individual_metadata) |
| 26 | 26 |
| 27 p1 = Population() | 27 p1 = Population() |
| 50 args.append(discard_fixed) | 50 args.append(discard_fixed) |
| 51 args.append(biased) | 51 args.append(biased) |
| 52 | 52 |
| 53 columns = p1.column_list() | 53 columns = p1.column_list() |
| 54 for column in columns: | 54 for column in columns: |
| 55 if input_type == 'gd_genotype': | |
| 56 column = int(column) - 2 | |
| 55 args.append('{0}:1'.format(column)) | 57 args.append('{0}:1'.format(column)) |
| 56 | 58 |
| 57 columns = p2.column_list() | 59 columns = p2.column_list() |
| 58 for column in columns: | 60 for column in columns: |
| 61 if input_type == 'gd_genotype': | |
| 62 column = int(column) - 2 | |
| 59 args.append('{0}:2'.format(column)) | 63 args.append('{0}:2'.format(column)) |
| 60 | 64 |
| 61 fh = open(output, 'w') | 65 fh = open(output, 'w') |
| 62 | 66 |
| 63 #print "args:", ' '.join(args) | 67 #print "args:", ' '.join(args) |