# HG changeset patch # User iuc # Date 1681632918 0 # Node ID 62359a1515218c63324dfe3c262dbfe930780346 # Parent 625fd9476402fb2328341440ebafef9f85200c97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 18d696a933873372ae5c77257fd31eaf2cd4ed13 diff -r 625fd9476402 -r 62359a151521 data_manager/twobit_builder.py --- a/data_manager/twobit_builder.py Sun Nov 22 12:54:42 2020 +0000 +++ b/data_manager/twobit_builder.py Sun Apr 16 08:15:18 2023 +0000 @@ -26,11 +26,14 @@ return sequence_id, sequence_name -def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name): +def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, long): twobit_base_name = "%s.2bit" % (sequence_id) twobit_filename = os.path.join(target_directory, twobit_base_name) - args = ['faToTwoBit', fasta_filename, twobit_filename] + args = ['faToTwoBit'] + if long: + args.append('-long') + args.extend([fasta_filename, twobit_filename]) tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-twobit-builder-stderr") proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno()) return_code = proc.wait() @@ -42,7 +45,7 @@ chunk = tmp_stderr.read(CHUNK_SIZE) if not chunk: break - sys.stderr.write(chunk) + sys.stderr.write(chunk.decode('utf-8')) sys.exit(return_code) tmp_stderr.close() # lastz_seqs @@ -71,6 +74,8 @@ parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename') parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey') parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description') + parser.add_option('-l', '--long', dest='long', action="store_true", default=False, help='For big genomes you need to pass the -long option.') + (options, args) = parser.parse_args() filename = args[0] @@ -90,7 +95,7 @@ sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description) # build the index - build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name) + build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.long) # save info to json file with open(filename, 'w') as fh: diff -r 625fd9476402 -r 62359a151521 data_manager/twobit_builder.xml --- a/data_manager/twobit_builder.xml Sun Nov 22 12:54:42 2020 +0000 +++ b/data_manager/twobit_builder.xml Sun Apr 16 08:15:18 2023 +0000 @@ -1,4 +1,4 @@ - + ucsc-fatotwobit python @@ -7,6 +7,7 @@ + diff -r 625fd9476402 -r 62359a151521 data_manager_conf.xml --- a/data_manager_conf.xml Sun Nov 22 12:54:42 2020 +0000 +++ b/data_manager_conf.xml Sun Apr 16 08:15:18 2023 +0000 @@ -1,7 +1,7 @@ - +