diff modify_snp_table.py @ 12:4b6590dd7250

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/modify_snp_table.py	Wed Sep 12 17:10:26 2012 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+import sys
+import subprocess
+from Population import Population
+
+################################################################################
+
+if len(sys.argv) < 9:
+    print >> sys.stderr, "Usage"
+    sys.exit(1)
+
+input, p1_input, output, lo, hi, lo_ind, lo_ind_qual = sys.argv[1:8]
+individual_metadata = sys.argv[8:]
+
+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 the population that is not in the SNP table'
+    sys.exit(1)
+
+################################################################################
+
+prog = 'pop'
+
+args = []
+args.append(prog)
+args.append(input)
+args.append(lo)
+args.append(hi)
+args.append(lo_ind)
+args.append(lo_ind_qual)
+
+columns = p1.column_list()
+
+for column in sorted(columns):
+    args.append(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)
+