diff data_manager/bwameth_index_builder.py @ 1:f5a15a12a4c9 draft default tip

Uploaded

--- a/data_manager/bwameth_index_builder.py	Thu Sep 15 04:59:28 2016 -0400
+++ b/data_manager/bwameth_index_builder.py	Thu Sep 15 05:58:04 2016 -0400
@@ -11,14 +11,14 @@
 DEFAULT_DATA_TABLE_NAME = "bwameth_indexes"
 
 
-def build_hisat_index(data_manager_dict, params, args):
+def build_bwameth_index(data_manager_dict, params, args):
     data_table_name = args.data_table_name
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     if not os.path.exists( target_directory ):
         os.mkdir( target_directory )
     fasta_base_name = os.path.basename(args.fasta_filename)
     sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
-    os.symlink(options.fasta_filename, sym_linked_fasta_filename)
+    os.symlink(args.fasta_filename, sym_linked_fasta_filename)
     args = ['bwameth.py', 'index', sym_linked_fasta_filename]
     proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
     return_code = proc.wait()
@@ -55,7 +55,7 @@
         raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey))
 
     # build the index
-    build_hisat_index(data_manager_dict, args)
+    build_bwameth_index(data_manager_dict, params, args)
 
     # save info to json file
     open(filename, 'wb').write(dumps(data_manager_dict))