Mercurial > repos > dfornika > mentalist

comparison data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py @ 0:1d9e3950ce61 draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
author dfornika
date Wed, 20 Dec 2017 17:36:03 -0500
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-1:000000000000 0:1d9e3950ce61
1 #!/usr/bin/env python
2 from __future__ import print_function
3
4 import argparse
5 import os
6 import subprocess
7 import sys
8 import errno
9 from json import dumps, loads
10
11 DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"]
12
13
14 def mentalist_build_db( data_manager_dict, database_name, kmer_size, profile, fasta_files, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
15 args = [ 'mentalist', 'build_db', '--db', database_name, '-k', str(kmer_size)]
16 if profile:
17 args += ['--profile', profile]
18 print(args)
19 args += ['--fasta_files'] + fasta_files
20 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
21 return_code = proc.wait()
22 if return_code:
23 print("Error building database.", file=sys.stderr)
24 sys.exit( return_code )
25 data_table_entry = dict( value=database_name, dbkey=database_name, name=database_name, path=database_name )
26 for data_table_name in data_table_names:
27 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
28
29
30 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
31 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
32 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
33 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
34 return data_manager_dict
35
36
37 def main():
38 parser = argparse.ArgumentParser()
39 parser.add_argument('params')
40 parser.add_argument( '-d', '--db', dest='database_name', default=None, help='Database Name' )
41 parser.add_argument( '-f', '--fasta_files', dest='fasta_files', nargs='+', default=None, help='FASTA Filenames' )
42 parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' )
43 parser.add_argument( '-p', '--profile', dest='profile', type=int, default=None, help='Profile' )
44 args = parser.parse_args()
45
46 params = loads( open( args.params ).read() )
47 target_directory = params[ 'output_data' ][0]['extra_files_path']
48
49 try:
50 os.mkdir( target_directory )
51 except OSError as exc:
52 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
53 pass
54 else:
55 raise
56
57 data_manager_dict = {}
58
59 # build the index
60 mentalist_build_db( data_manager_dict, args.database_name, args.kmer_size, args.profile, args.fasta_files, params, target_directory, DEFAULT_DATA_TABLE_NAMES )
61
62 # save info to json file
63 open( args.params, 'wb' ).write( dumps( data_manager_dict ) )
64
65
66 if __name__ == "__main__":
67 main()