diff add_fst_column.py @ 0:2c498d40ecde

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_fst_column.py	Mon Apr 09 12:03:06 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)
+