Mercurial > repos > iuc > data_manager_bwameth_index_builder
comparison data_manager/bwameth_index_builder.py @ 0:a7fb84abef45 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
author | iuc |
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date | Tue, 22 Nov 2016 17:12:00 -0500 |
parents | |
children | e7ca32457e36 |
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-1:000000000000 | 0:a7fb84abef45 |
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1 #!/usr/bin/env python | |
2 # Based heavily on the HISAT2 data manager wrapper | |
3 | |
4 import argparse | |
5 import os | |
6 import subprocess | |
7 import sys | |
8 from json import dumps, loads | |
9 | |
10 DEFAULT_DATA_TABLE_NAME = "bwameth_indexes" | |
11 | |
12 | |
13 def build_bwameth_index(data_manager_dict, params, args): | |
14 data_table_name = args.data_table_name | |
15 target_directory = params[ 'output_data' ][0]['extra_files_path'] | |
16 if not os.path.exists( target_directory ): | |
17 os.mkdir( target_directory ) | |
18 fasta_base_name = os.path.basename(args.fasta_filename) | |
19 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name) | |
20 os.symlink(os.path.abspath(args.fasta_filename), sym_linked_fasta_filename) | |
21 cmd = ['bwameth.py', 'index', sym_linked_fasta_filename] | |
22 proc = subprocess.Popen(args=cmd, shell=False, cwd=target_directory) | |
23 return_code = proc.wait() | |
24 if return_code: | |
25 print >> sys.stderr, "Error building index." | |
26 sys.exit( return_code ) | |
27 data_table_entry = dict(value=args.dbKey, dbkey=args.dbkey, name=args.name, path=args.dbKey) | |
28 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) | |
29 | |
30 | |
31 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): | |
32 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | |
33 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) | |
34 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) | |
35 return data_manager_dict | |
36 | |
37 | |
38 def main(): | |
39 # Parse Command Line | |
40 parser = argparse.ArgumentParser() | |
41 parser.add_argument( '--output', default=None ) | |
42 parser.add_argument( '--fasta_filename', default=None ) | |
43 parser.add_argument( '--dbkey', default=None ) | |
44 parser.add_argument( '--name', default=None ) | |
45 parser.add_argument( '--description', default=None ) | |
46 parser.add_argument( '--data_table_name', default=DEFAULT_DATA_TABLE_NAME ) | |
47 args = parser.parse_args() | |
48 | |
49 filename = args.output | |
50 params = loads(open(filename).read()) | |
51 data_manager_dict = {} | |
52 | |
53 if args.dbkey in [ None, '', '?' ]: | |
54 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey)) | |
55 | |
56 # build the index | |
57 build_bwameth_index(data_manager_dict, params, args) | |
58 | |
59 # save info to json file | |
60 open(filename, 'wb').write(dumps(data_manager_dict)) | |
61 | |
62 | |
63 if __name__ == "__main__": | |
64 main() |