Mercurial > repos > devteam > data_manager_twobit_builder
diff data_manager/twobit_builder.py @ 7:94a50db37d1a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
| author | iuc |
|---|---|
| date | Sun, 16 Apr 2023 08:31:43 +0000 |
| parents | 62359a151521 |
| children |
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--- a/data_manager/twobit_builder.py Sun Apr 16 08:15:18 2023 +0000 +++ b/data_manager/twobit_builder.py Sun Apr 16 08:31:43 2023 +0000 @@ -26,14 +26,11 @@ return sequence_id, sequence_name -def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, long): +def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name): twobit_base_name = "%s.2bit" % (sequence_id) twobit_filename = os.path.join(target_directory, twobit_base_name) - args = ['faToTwoBit'] - if long: - args.append('-long') - args.extend([fasta_filename, twobit_filename]) + args = ['faToTwoBit', 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() @@ -45,7 +42,7 @@ chunk = tmp_stderr.read(CHUNK_SIZE) if not chunk: break - sys.stderr.write(chunk.decode('utf-8')) + sys.stderr.write(chunk) sys.exit(return_code) tmp_stderr.close() # lastz_seqs @@ -74,8 +71,6 @@ 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] @@ -95,7 +90,7 @@ 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, options.long) + build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name) # save info to json file with open(filename, 'w') as fh: