diff offspring_heterozygosity_pedigree.py @ 31:a631c2f6d913

Update to Miller Lab devshed revision 3c4110ffacc3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/offspring_heterozygosity_pedigree.py	Fri Sep 20 13:25:27 2013 -0400
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+import sys
+import gd_util
+
+from Population import Population
+
+def load_and_check_pop(file, total_pop, name):
+        p = Population()
+        p.from_population_file(file)
+        if not total_pop.is_superset(p):
+            gd_util.die('There is an individual in the {0} that is not in the SNP table'.format(name))
+        return p
+
+def append_breeders_from_file(the_list, filename, kind):
+        with open(filename) as fh:
+            for line in fh:
+                elems = line.split()
+                breeder = elems[0].rstrip('\r\n')
+                the_list.append('{0}:{1}'.format(kind, breeder))
+
+################################################################################
+
+if len(sys.argv) != 9:
+    gd_util.die('Usage')
+
+input, input_type, pedigree, ind_arg, founders, b1_input, b2_input, output = sys.argv[1:]
+
+p_total = Population()
+p_total.from_wrapped_dict(ind_arg)
+
+f1 = load_and_check_pop(founders, p_total, 'founders')
+
+################################################################################
+
+prog = 'offspring_heterozygosity2'
+
+args = [ prog ]
+args.append(input)      # a Galaxy SNP table
+args.append(pedigree)   # a pedigree, where the SNP table is for the founders
+
+for tag in f1.tag_list():
+    column, name = tag.split(':')
+    if type == 'gd_genotype':
+        column = int(column) - 2
+    tag = 'founder:{0}:{1}'.format(column, name)
+    args.append(tag)
+
+append_breeders_from_file(args, b1_input, 0)
+append_breeders_from_file(args, b2_input, 1)
+
+with open(output, 'w') as fh:
+    gd_util.run_program(prog, args, stdout=fh)
+
+################################################################################
+
+sys.exit(0)
+