Mercurial > repos > miller-lab > genome_diversity
diff offspring_heterozygosity.py @ 31:a631c2f6d913
Update to Miller Lab devshed revision 3c4110ffacc3
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Fri, 20 Sep 2013 13:25:27 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/offspring_heterozygosity.py Fri Sep 20 13:25:27 2013 -0400 @@ -0,0 +1,59 @@ +#!/usr/bin/env python + +import sys +import gd_util + +from Population import Population + +################################################################################ + +if len(sys.argv) != 7: + gd_util.die('Usage') + +input, input_type, ind_arg, p1_input, p2_input, output = sys.argv[1:] + +p_total = Population() +p_total.from_wrapped_dict(ind_arg) + +p1 = Population() +p1.from_population_file(p1_input) +if not p_total.is_superset(p1): + gd_util.die('There is an individual in the first population that is not in the SNP table') + +p2 = Population() +p2.from_population_file(p2_input) +if not p_total.is_superset(p2): + gd_util.die('There is an individual in the second population that is not in the SNP table') + +################################################################################ + +prog = 'offspring_heterozygosity' + +args = [ prog ] +args.append(input) # a Galaxy SNP table + +for tag in p1.tag_list(): + column, name = tag.split(':') + + if input_type == 'gd_genotype': + column = int(column) - 2 + + tag = '{0}:{1}:{2}'.format(column, 0, name) + args.append(tag) + +for tag in p2.tag_list(): + column, name = tag.split(':') + + if input_type == 'gd_genotype': + column = int(column) - 2 + + tag = '{0}:{1}:{2}'.format(column, 1, name) + args.append(tag) + +with open(output, 'w') as fh: + gd_util.run_program(prog, args, stdout=fh) + +################################################################################ + +sys.exit(0) +