diff average_fst.py @ 24:248b06e86022

Added gd_genotype datatype. Modified tools to support new datatype.

--- a/average_fst.py	Wed May 22 15:58:18 2013 -0400
+++ b/average_fst.py	Tue May 28 16:24:19 2013 -0400
@@ -6,12 +6,12 @@
 
 ################################################################################
 
-if len(sys.argv) < 11:
+if len(sys.argv) < 12:
     print >> sys.stderr, "Usage"
     sys.exit(1)
 
-input, p1_input, p2_input, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:10]
-individual_metadata = sys.argv[10:]
+input, p1_input, p2_input, input_type, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:11]
+individual_metadata = sys.argv[11:]
 
 try:
     shuffle_count = int(shuffles)
@@ -55,15 +55,21 @@
 
 columns = p1.column_list()
 for column in columns:
+    if input_type == 'gd_genotype':
+        column = int(column) - 2
     args.append('{0}:1'.format(column))
 
 columns = p2.column_list()
 for column in columns:
+    if input_type == 'gd_genotype':
+        column = int(column) - 2
     args.append('{0}:2'.format(column))
 
 if p0 is not None:
     columns = p0.column_list()
     for column in columns:
+        if input_type == 'gd_genotype':
+            column = int(column) - 2
         args.append('{0}:0'.format(column))
 
 fh = open(output, 'w')