Mercurial > repos > miller-lab > genome_diversity
comparison average_fst.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 | f04f40a36cc8 |
| children | 8997f2ca8c7a |
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| 23:66a183c44dd5 | 24:248b06e86022 |
|---|---|
| 4 import subprocess | 4 import subprocess |
| 5 from Population import Population | 5 from Population import Population |
| 6 | 6 |
| 7 ################################################################################ | 7 ################################################################################ |
| 8 | 8 |
| 9 if len(sys.argv) < 11: | 9 if len(sys.argv) < 12: |
| 10 print >> sys.stderr, "Usage" | 10 print >> sys.stderr, "Usage" |
| 11 sys.exit(1) | 11 sys.exit(1) |
| 12 | 12 |
| 13 input, p1_input, p2_input, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:10] | 13 input, p1_input, p2_input, input_type, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:11] |
| 14 individual_metadata = sys.argv[10:] | 14 individual_metadata = sys.argv[11:] |
| 15 | 15 |
| 16 try: | 16 try: |
| 17 shuffle_count = int(shuffles) | 17 shuffle_count = int(shuffles) |
| 18 except: | 18 except: |
| 19 shuffle_count = 0 | 19 shuffle_count = 0 |
| 53 args.append(discard_fixed) | 53 args.append(discard_fixed) |
| 54 args.append(shuffles) | 54 args.append(shuffles) |
| 55 | 55 |
| 56 columns = p1.column_list() | 56 columns = p1.column_list() |
| 57 for column in columns: | 57 for column in columns: |
| 58 if input_type == 'gd_genotype': | |
| 59 column = int(column) - 2 | |
| 58 args.append('{0}:1'.format(column)) | 60 args.append('{0}:1'.format(column)) |
| 59 | 61 |
| 60 columns = p2.column_list() | 62 columns = p2.column_list() |
| 61 for column in columns: | 63 for column in columns: |
| 64 if input_type == 'gd_genotype': | |
| 65 column = int(column) - 2 | |
| 62 args.append('{0}:2'.format(column)) | 66 args.append('{0}:2'.format(column)) |
| 63 | 67 |
| 64 if p0 is not None: | 68 if p0 is not None: |
| 65 columns = p0.column_list() | 69 columns = p0.column_list() |
| 66 for column in columns: | 70 for column in columns: |
| 71 if input_type == 'gd_genotype': | |
| 72 column = int(column) - 2 | |
| 67 args.append('{0}:0'.format(column)) | 73 args.append('{0}:0'.format(column)) |
| 68 | 74 |
| 69 fh = open(output, 'w') | 75 fh = open(output, 'w') |
| 70 | 76 |
| 71 #print "args:", ' '.join(args) | 77 #print "args:", ' '.join(args) |