diff data_manager/rnastar_index_builder.py @ 2:8a2d16bfdae2 draft

Uploaded

--- a/data_manager/rnastar_index_builder.py	Mon Sep 29 20:47:45 2014 -0400
+++ b/data_manager/rnastar_index_builder.py	Fri Oct 03 21:59:39 2014 -0400
@@ -9,7 +9,7 @@
 import optparse
 import subprocess
 
-from galaxy.util.json import from_json_string, to_json_string
+from json import loads, dumps
 
 DEFAULT_DATA_TABLE_NAME = "rnastar_indexes"
 
@@ -44,20 +44,11 @@
    --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' %  pdict
     elif sjdbFileChrStartEnd:
         cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict
-    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" )
     args = cl.split(' ')
-    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
+    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
     return_code = proc.wait()
     if return_code:
-        tmp_stderr.flush()
-        tmp_stderr.seek(0)
-        print >> sys.stderr, "Error building index: retcode=",retcode
-        while True:
-            chunk = tmp_stderr.read( CHUNK_SIZE )
-            if not chunk:
-                break
-            sys.stderr.write( chunk )
-    tmp_stderr.close()
+        sys.exit( return_code )
     data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
     _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
 
@@ -86,9 +77,9 @@
     (options, args) = parser.parse_args()
     
     filename = options.out_file
-    params = from_json_string( open( filename ).read() )
+    params = loads( open( filename ).read() )
     target_directory = options.out_index_path
-    os.mkdir( target_directory )
+    os.mkdirs( target_directory )
     data_manager_dict = {}
     
     dbkey = options.fasta_dbkey
@@ -107,6 +98,6 @@
 
     
     #save info to json file
-    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
         
 if __name__ == "__main__": main()