diff data_manager/data_manager_snpEff_databases.py @ 5:3d9dd4b9fb09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty

--- a/data_manager/data_manager_snpEff_databases.py	Tue Apr 04 18:14:37 2017 -0400
+++ b/data_manager/data_manager_snpEff_databases.py	Tue Apr 18 09:40:03 2017 -0400
@@ -6,33 +6,20 @@
 import sys
 
 
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit(1)
-
-
-def fetch_databases(data_manager_dict, target_directory, jar_path):
-    (snpEff_dir, snpEff_jar) = os.path.split(jar_path)
+def fetch_databases(data_manager_dict, target_directory):
     if not os.path.exists(target_directory):
         os.makedirs(target_directory)
     databases_path = os.path.join( target_directory, 'databases.out' )
     databases_output = open(databases_path, 'w')
-    args = [ 'java', '-jar' ]
-    args.append( snpEff_jar )
-    args.append( 'databases' )
-    # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" )
-    # databases_output = open(databases_path)
-    # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() )
-    proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() )
-    return_code = proc.wait()
+    args = ['snpEff', 'databases']
+    return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
     if return_code:
         sys.exit( return_code )
     databases_output.close()
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
     data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
     data_table_entries = []
-    try:
-        fh = open(databases_path, 'r')
+    with open(databases_path, 'r') as fh:
         for i, line in enumerate(fh):
             fields = line.split('\t')
             if len(fields) >= 2:
@@ -45,17 +32,11 @@
                 description = fields[1].strip() + ' : ' + genome_version
                 data_table_entries.append(dict(value=genome_version, name=description))
         data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries
-    except Exception as e:
-        stop_err( 'Error parsing %s %s\n' % (databases_path, str( e )) )
-    else:
-        fh.close()
     return data_manager_dict
 
 
 def main():
-    # Parse Command Line
     parser = optparse.OptionParser()
-    parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' )
     (options, args) = parser.parse_args()
 
     filename = args[0]
@@ -66,7 +47,7 @@
     data_manager_dict = {}
 
     # Create Defuse Reference Data
-    data_manager_dict = fetch_databases( data_manager_dict, target_directory, options.jar_path)
+    data_manager_dict = fetch_databases( data_manager_dict, target_directory)
 
     # save info to json file
     open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )