Remove genetic code option from getref

ariba/ref_genes_getter.py

@@ -25,11 +25,11 @@ class Error (Exception): pass
 
 
 class RefGenesGetter:
-    def __init__(self, ref_db, genetic_code=11, version=None):
+    def __init__(self, ref_db, version=None):
         if ref_db not in allowed_ref_dbs:
             raise Error('Error in RefGenesGetter. ref_db must be one of: ' + str(allowed_ref_dbs) + ', but I got "' + ref_db)
         self.ref_db=ref_db
-        self.genetic_code = genetic_code
+        self.genetic_code = 11
         self.max_download_attempts = 3
         self.sleep_time = 2
         self.version = version

ariba/tasks/getref.py

@@ -5,7 +5,6 @@
 def run(options):
     getter = ref_genes_getter.RefGenesGetter(
         options.db,
-        genetic_code=options.genetic_code,
         version=options.version
     )
     getter.run(options.outprefix)

scripts/ariba

@@ -49,7 +49,6 @@ subparser_getref = subparsers.add_parser(
     usage='ariba getref [options] <db> <outprefix>',
     description='Download reference data from one of a few supported public resources',
 )
-subparser_getref.add_argument('--genetic_code', type=int, help='Number of genetic code to use. Currently supported 1,4,11 [%(default)s]', choices=[1,4,11], default=11, metavar='INT')
 subparser_getref.add_argument('--version', help='Version of reference data to download. If not used, gets the latest version. Only applies to card')
 subparser_getref.add_argument('db', help='Database to download. Must be one of: ' + ' '.join(allowed_dbs), choices=allowed_dbs, metavar="DB name")
 subparser_getref.add_argument('outprefix', help='Prefix of output filenames')