diff dpmix.py @ 24:248b06e86022

Added gd_genotype datatype. Modified tools to support new datatype.

--- a/dpmix.py	Wed May 22 15:58:18 2013 -0400
+++ b/dpmix.py	Tue May 28 16:24:19 2013 -0400
@@ -41,12 +41,12 @@
 
 ################################################################################
 
-if len(sys.argv) < 15:
+if len(sys.argv) < 16:
     print "usage"
     sys.exit(1)
 
-input, data_source, switch_penalty, ap1_input, ap2_input, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir, heterochromatin_loc_file = sys.argv[1:14]
-individual_metadata = sys.argv[14:]
+input, input_type, data_source, switch_penalty, ap1_input, ap2_input, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir, heterochromatin_loc_file = sys.argv[1:15]
+individual_metadata = sys.argv[15:]
 
 chrom = 'all'
 add_logs = '0'
@@ -104,15 +104,24 @@
 
 columns = ap1.column_list()
 for column in columns:
-    args.append('{0}:1:{1}'.format(column, ap1.individual_with_column(column).name))
+    if input_type == 'gd_genotype':
+        args.append('{0}:1:{1}'.format(int(column) - 2, ap1.individual_with_column(column).name))
+    else:
+        args.append('{0}:1:{1}'.format(column, ap1.individual_with_column(column).name))
 
 columns = ap2.column_list()
 for column in columns:
-    args.append('{0}:2:{1}'.format(column, ap2.individual_with_column(column).name))
+    if input_type == 'gd_genotype':
+        args.append('{0}:2:{1}'.format(int(column) - 2, ap2.individual_with_column(column).name))
+    else:
+        args.append('{0}:2:{1}'.format(column, ap2.individual_with_column(column).name))
 
 columns = p.column_list()
 for column in columns:
-    args.append('{0}:0:{1}'.format(column, p.individual_with_column(column).name))
+    if input_type == 'gd_genotype':
+        args.append('{0}:0:{1}'.format(int(column) - 2, p.individual_with_column(column).name))
+    else:
+        args.append('{0}:0:{1}'.format(column, p.individual_with_column(column).name))
 
 run_program(None, args, stdout_file=output, space_to_tab=True)