Mercurial > repos > dfornika > data_manager_build_bracken_database
comparison data_manager/bracken_build_database.py @ 0:911bb6c95bf8 draft default tip
"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_bracken_database/ commit d0b060e7d9cc9fd89926dbc07fc93c8a1471b3fe-dirty"
author | dfornika |
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date | Thu, 24 Oct 2019 17:44:45 -0400 |
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-1:000000000000 | 0:911bb6c95bf8 |
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1 #!/usr/bin/env python | |
2 | |
3 from __future__ import print_function | |
4 | |
5 import argparse | |
6 import errno | |
7 import json | |
8 import os | |
9 import subprocess | |
10 import uuid | |
11 | |
12 | |
13 DATA_TABLE_NAME = "bracken_databases" | |
14 | |
15 | |
16 def bracken_build_database(target_directory, bracken_build_args, database_name, data_table_name=DATA_TABLE_NAME): | |
17 | |
18 database_value = str(uuid.uuid4()) | |
19 | |
20 database_name = database_name | |
21 | |
22 database_path = os.path.join(bracken_build_args['kraken_database'], 'database' + str(bracken_build_args['read_len']) + 'mers.kmer_distrib') | |
23 | |
24 bracken_build_args_list = [ | |
25 '-t', bracken_build_args['threads'], | |
26 '-k', bracken_build_args['kmer_len'], | |
27 '-l', bracken_build_args['read_len'], | |
28 '-d', bracken_build_args['kraken_database'], | |
29 ] | |
30 | |
31 subprocess.check_call(['bracken-build'] + bracken_build_args_list) | |
32 | |
33 data_table_entry = { | |
34 "data_tables": { | |
35 data_table_name: [ | |
36 { | |
37 "value": database_value, | |
38 "name": database_name, | |
39 "path": database_path, | |
40 } | |
41 ] | |
42 } | |
43 } | |
44 | |
45 return data_table_entry | |
46 | |
47 | |
48 def main(): | |
49 parser = argparse.ArgumentParser() | |
50 parser.add_argument('data_manager_json') | |
51 parser.add_argument('--threads', dest='threads', default=1, help='threads') | |
52 parser.add_argument('--kmer-len', dest='kmer_len', help='K-mer length') | |
53 parser.add_argument('--read-len', dest='read_len', help='Read length') | |
54 parser.add_argument('--kraken-db', dest='kraken_database', help='Kraken Database') | |
55 parser.add_argument('--database-name', dest='database_name', help='Database Name') | |
56 args = parser.parse_args() | |
57 | |
58 data_manager_input = json.loads(open(args.data_manager_json).read()) | |
59 | |
60 target_directory = data_manager_input['output_data'][0]['extra_files_path'] | |
61 | |
62 bracken_build_args = { | |
63 'threads': args.threads, | |
64 'kmer_len': args.kmer_len, | |
65 'read_len': args.read_len, | |
66 'kraken_database': args.kraken_database, | |
67 } | |
68 | |
69 try: | |
70 os.mkdir(target_directory) | |
71 except OSError as exc: | |
72 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): | |
73 pass | |
74 else: | |
75 raise | |
76 | |
77 data_manager_output = {} | |
78 | |
79 data_manager_output = bracken_build_database( | |
80 target_directory, | |
81 bracken_build_args, | |
82 args.database_name, | |
83 ) | |
84 | |
85 with open(args.data_manager_json, 'w') as out: | |
86 out.write(json.dumps(data_manager_output, sort_keys=True)) | |
87 | |
88 | |
89 if __name__ == "__main__": | |
90 main() |