diff data_manager/bwameth_index_builder.py @ 0:a801458261bb draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bwameth_index_builder.py	Thu Sep 15 04:59:28 2016 -0400
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+# Based heavily on the HISAT2 data manager wrapper
+
+import argparse
+import os
+import shlex
+import subprocess
+import sys
+from json import dumps, loads
+
+DEFAULT_DATA_TABLE_NAME = "bwameth_indexes"
+
+
+def build_hisat_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)
+    args = ['bwameth.py', 'index', sym_linked_fasta_filename]
+    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+    return_code = proc.wait()
+    if return_code:
+        print >> sys.stderr, "Error building index."
+        sys.exit( return_code )
+    data_table_entry = dict(value=args.name, dbkey=args.dbkey, name=args.name, path=sequence_id)
+    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+
+
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+    data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+    return data_manager_dict
+
+
+def main():
+    # Parse Command Line
+    parser = argparse.ArgumentParser()
+    parser.add_argument( '--output', default=None )
+    parser.add_argument( '--fasta_filename', default=None )
+    parser.add_argument( '--dbkey', default=None )
+    parser.add_argument( '--name', default=None )
+    parser.add_argument( '--description', default=None )
+    parser.add_argument( '--data_table_name', default=DEFAULT_DATA_TABLE_NAME )
+    args = parser.parse_args()
+
+    filename = args.output
+    params = loads(open(filename).read())
+    data_manager_dict = {}
+
+    if args.dbkey in [ None, '', '?' ]:
+        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)
+
+    # save info to json file
+    open(filename, 'wb').write(dumps(data_manager_dict))
+
+if __name__ == "__main__":
+    main()