--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/hisat2_index_builder.py	Sat Oct 10 14:53:43 2015 -0400
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+# Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg
+
+import shlex
+import sys
+import os
+import argparse
+import subprocess
+
+from json import loads, dumps
+
+
+DEFAULT_DATA_TABLE_NAME = "hisat2_indexes"
+
+
+def get_id_name( params, dbkey, fasta_description=None):
+    # TODO: ensure sequence_id is unique and does not already appear in location file
+    sequence_id = params['param_dict']['sequence_id']
+    if not sequence_id:
+        sequence_id = dbkey
+
+    sequence_name = params['param_dict']['sequence_name']
+    if not sequence_name:
+        sequence_name = fasta_description
+        if not sequence_name:
+            sequence_name = dbkey
+    return sequence_id, sequence_name
+
+
+def build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name ):
+    data_table_name = options.data_table_name or DEFAULT_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.split( options.fasta_filename )[-1]
+    sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
+    os.symlink( options.fasta_filename, sym_linked_fasta_filename )
+    args = [ 'hisat2-build' ]
+    args.extend( shlex.split( options.indexer_options ) )
+    args.extend( [ sym_linked_fasta_filename, sequence_id ] )
+    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=sequence_id, dbkey=options.fasta_dbkey, name=sequence_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', dest='output', action='store', type=str, default=None )
+    parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None )
+    parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None )
+    parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None )
+    parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes' )
+    parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, required=True, default=None )
+    options = parser.parse_args()
+
+    filename = options.output
+
+    params = loads( open( filename ).read() )
+    data_manager_dict = {}
+
+    if options.fasta_dbkey in [ None, '', '?' ]:
+        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
+
+    sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
+
+    # build the index
+    build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name )
+
+    # save info to json file
+    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+
+if __name__ == "__main__":
+    main()