Mercurial > repos > miller-lab > genome_diversity
diff add_fst_column.py @ 14:8ae67e9fb6ff
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 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/add_fst_column.py Fri Sep 28 11:35:56 2012 -0400 @@ -0,0 +1,69 @@ +#!/usr/bin/env python + +# <command interpreter="python"> +# add_fst_column.py "$input" "$p1_input" "$p2_input" "$data_source.choice" "$data_source.min_value" "$retain" "$discard_fixed" "$biased" "$output" +# #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) +# #set $arg = '%s:%s' % ($individual_col, $individual) +# "$arg" +# #end for +# </command> + +import sys +import subprocess +from Population import Population + +################################################################################ + +if len(sys.argv) < 12: + print >> sys.stderr, "Usage" + sys.exit(1) + +input, p1_input, p2_input, genotypes, min_reads, min_qual, retain, discard_fixed, biased, output = sys.argv[1:11] +individual_metadata = sys.argv[11:] + +p_total = Population() +p_total.from_tag_list(individual_metadata) + +p1 = Population() +p1.from_population_file(p1_input) +if not p_total.is_superset(p1): + print >> sys.stderr, 'There is an individual in population 1 that is not in the SNP table' + sys.exit(1) + +p2 = Population() +p2.from_population_file(p2_input) +if not p_total.is_superset(p2): + print >> sys.stderr, 'There is an individual in population 2 that is not in the SNP table' + sys.exit(1) + +################################################################################ + +prog = 'Fst_column' + +args = [] +args.append(prog) +args.append(input) +args.append(genotypes) +args.append(min_reads) +args.append(min_qual) +args.append(retain) +args.append(discard_fixed) +args.append(biased) + +columns = p1.column_list() +for column in columns: + args.append('{0}:1'.format(column)) + +columns = p2.column_list() +for column in columns: + args.append('{0}:2'.format(column)) + +fh = open(output, 'w') + +#print "args:", ' '.join(args) +p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr) +rc = p.wait() +fh.close() + +sys.exit(0) +