Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder

diff data_manager/novocraft_index_builder.py @ 12:283eec05d1de draft
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit e14dbfe322e3787d1ec9b7467a3677b101784227
author: sanbi-uwc
date: Tue, 08 Mar 2016 05:38:52 -0500
parents: a9b725202132
children: d053e7b179b5
--- a/data_manager/novocraft_index_builder.py	Mon Mar 07 02:27:51 2016 -0500
+++ b/data_manager/novocraft_index_builder.py	Tue Mar 08 05:38:52 2016 -0500
@@ -37,13 +37,14 @@
     elif not os.path.exists(target_directory):
         os.mkdir(target_directory)
 
-    index_filename = os.path.join(target_directory,"%.nix" % sequence_id)
+    print(sequence_id)
+    nix_file = sequence_id + ".nix"
+    index_filename = os.path.join(target_directory, nix_file)
     cmdline_str = 'novoindex {} {}'.format(index_filename, fasta_filename)
     cmdline = shlex.split(cmdline_str)
 
-    #index_filename = 'foo'
-    #cmdline = ('touch', '{}/{}'.format(target_directory, index_filename))
     try:
+        print(cmdline)
         check_call(cmdline)
     except CalledProcessError:
         print("Error building RNA STAR index", file=sys.stderr)
@@ -83,7 +84,7 @@
 
     params = loads(open(filename).read())
     target_directory = params['output_data'][0]['extra_files_path']
-    os.makedirs(target_directory)
+    #os.makedirs(target_directory)
     data_manager_dict = {}
 
     dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description)