Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
changeset 4:ef2031036f47 draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Mon, 26 Nov 2018 10:53:58 -0500 |
| parents | 3d12fd3b7cae |
| children | 3888ec1918d0 |
| files | data_manager/salmon_index_builder.py |
| diffstat | 1 files changed, 2 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/salmon_index_builder.py Fri Oct 19 10:26:13 2018 -0400 +++ b/data_manager/salmon_index_builder.py Mon Nov 26 10:53:58 2018 -0500 @@ -34,8 +34,8 @@ if options.kmer_size != '': args.append('-k') args.append(options.kmer_size) - args.extend( [ '-t' , options.fasta_filename, '-i', sequence_id ] ) - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) + args.extend( [ '-t' , options.fasta_filename, '-i', target_directory ] ) + proc = subprocess.Popen( args=args, shell=False) return_code = proc.wait() if return_code: print("Error building index.", file=sys.stderr) @@ -71,7 +71,6 @@ raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) - # build the index build_salmon_index( data_manager_dict, options, params, sequence_id, sequence_name )