Mercurial > repos > devteam > data_manager_twobit_builder
comparison data_manager/twobit_builder.py @ 6:62359a151521 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 18d696a933873372ae5c77257fd31eaf2cd4ed13
author | iuc |
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date | Sun, 16 Apr 2023 08:15:18 +0000 |
parents | 625fd9476402 |
children | 94a50db37d1a |
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5:625fd9476402 | 6:62359a151521 |
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24 if not sequence_name: | 24 if not sequence_name: |
25 sequence_name = dbkey | 25 sequence_name = dbkey |
26 return sequence_id, sequence_name | 26 return sequence_id, sequence_name |
27 | 27 |
28 | 28 |
29 def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name): | 29 def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, long): |
30 twobit_base_name = "%s.2bit" % (sequence_id) | 30 twobit_base_name = "%s.2bit" % (sequence_id) |
31 twobit_filename = os.path.join(target_directory, twobit_base_name) | 31 twobit_filename = os.path.join(target_directory, twobit_base_name) |
32 | 32 |
33 args = ['faToTwoBit', fasta_filename, twobit_filename] | 33 args = ['faToTwoBit'] |
34 if long: | |
35 args.append('-long') | |
36 args.extend([fasta_filename, twobit_filename]) | |
34 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-twobit-builder-stderr") | 37 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-twobit-builder-stderr") |
35 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno()) | 38 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno()) |
36 return_code = proc.wait() | 39 return_code = proc.wait() |
37 if return_code: | 40 if return_code: |
38 tmp_stderr.flush() | 41 tmp_stderr.flush() |
40 print("Error building index:", file=sys.stderr) | 43 print("Error building index:", file=sys.stderr) |
41 while True: | 44 while True: |
42 chunk = tmp_stderr.read(CHUNK_SIZE) | 45 chunk = tmp_stderr.read(CHUNK_SIZE) |
43 if not chunk: | 46 if not chunk: |
44 break | 47 break |
45 sys.stderr.write(chunk) | 48 sys.stderr.write(chunk.decode('utf-8')) |
46 sys.exit(return_code) | 49 sys.exit(return_code) |
47 tmp_stderr.close() | 50 tmp_stderr.close() |
48 # lastz_seqs | 51 # lastz_seqs |
49 data_table_entry = dict(value=sequence_id, name=sequence_name, path=twobit_base_name) | 52 data_table_entry = dict(value=sequence_id, name=sequence_name, path=twobit_base_name) |
50 | 53 |
69 def main(): | 72 def main(): |
70 parser = optparse.OptionParser() | 73 parser = optparse.OptionParser() |
71 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename') | 74 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename') |
72 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey') | 75 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey') |
73 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description') | 76 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description') |
77 parser.add_option('-l', '--long', dest='long', action="store_true", default=False, help='For big genomes you need to pass the -long option.') | |
78 | |
74 (options, args) = parser.parse_args() | 79 (options, args) = parser.parse_args() |
75 | 80 |
76 filename = args[0] | 81 filename = args[0] |
77 | 82 |
78 with open(filename) as fh: | 83 with open(filename) as fh: |
88 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey)) | 93 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey)) |
89 | 94 |
90 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description) | 95 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description) |
91 | 96 |
92 # build the index | 97 # build the index |
93 build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name) | 98 build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.long) |
94 | 99 |
95 # save info to json file | 100 # save info to json file |
96 with open(filename, 'w') as fh: | 101 with open(filename, 'w') as fh: |
97 json.dump(data_manager_dict, fh, sort_keys=True) | 102 json.dump(data_manager_dict, fh, sort_keys=True) |
98 | 103 |