Mercurial > repos > iuc > data_manager_hisat2_index_builder

comparison data_manager/hisat2_index_builder.py @ 5:8eac26f44d29 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
author iuc
date Mon, 18 Nov 2019 17:22:30 -0500
parents d210e1f185bd
children a04cebcd77f4
comparison
equal deleted inserted replaced
4:d210e1f185bd 5:8eac26f44d29
10 from json import dumps, loads 10 from json import dumps, loads
11 11
12 DEFAULT_DATA_TABLE_NAME = "hisat2_indexes" 12 DEFAULT_DATA_TABLE_NAME = "hisat2_indexes"
13 13
14 14
15 def get_id_name( params, dbkey, fasta_description=None): 15 def get_id_name(params, dbkey, fasta_description=None):
16 # TODO: ensure sequence_id is unique and does not already appear in location file 16 # TODO: ensure sequence_id is unique and does not already appear in location file
17 sequence_id = params['param_dict']['sequence_id'] 17 sequence_id = params['param_dict']['sequence_id']
18 if not sequence_id: 18 if not sequence_id:
19 sequence_id = dbkey 19 sequence_id = dbkey
20 20
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_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name ): 29 def build_hisat_index(data_manager_dict, options, params, sequence_id, sequence_name):
30 data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME 30 data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
31 target_directory = params[ 'output_data' ][0]['extra_files_path'] 31 target_directory = params['output_data'][0]['extra_files_path']
32 if not os.path.exists( target_directory ): 32 if not os.path.exists(target_directory):
33 os.mkdir( target_directory ) 33 os.mkdir(target_directory)
34 fasta_base_name = os.path.split( options.fasta_filename )[-1] 34 fasta_base_name = os.path.split(options.fasta_filename)[-1]
35 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) 35 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
36 os.symlink( options.fasta_filename, sym_linked_fasta_filename ) 36 os.symlink(options.fasta_filename, sym_linked_fasta_filename)
37 args = [ 'hisat2-build' ] 37 args = ['hisat2-build']
38 args.extend( shlex.split( options.indexer_options ) ) 38 args.extend(shlex.split(options.indexer_options))
39 args.extend( [ sym_linked_fasta_filename, sequence_id ] ) 39 args.extend([sym_linked_fasta_filename, sequence_id])
40 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) 40 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
41 return_code = proc.wait() 41 return_code = proc.wait()
42 if return_code: 42 if return_code:
43 print("Error building index.", file=sys.stderr) 43 print("Error building index.", file=sys.stderr)
44 sys.exit( return_code ) 44 sys.exit(return_code)
45 data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id ) 45 data_table_entry = dict(value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id)
46 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) 46 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
47 47
48 48
49 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): 49 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
50 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 50 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
51 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) 51 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
52 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) 52 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
53 return data_manager_dict 53 return data_manager_dict
54 54
55 55
56 def main(): 56 def main():
57 # Parse Command Line 57 # Parse Command Line
58 parser = argparse.ArgumentParser() 58 parser = argparse.ArgumentParser()
59 parser.add_argument( '--output', dest='output', action='store', type=str, default=None ) 59 parser.add_argument('--output', dest='output', action='store', type=str, default=None)
60 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None ) 60 parser.add_argument('--fasta_filename', dest='fasta_filename', action='store', type=str, default=None)
61 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None ) 61 parser.add_argument('--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None)
62 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None ) 62 parser.add_argument('--fasta_description', dest='fasta_description', action='store', type=str, default=None)
63 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes' ) 63 parser.add_argument('--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes')
64 parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, default='' ) 64 parser.add_argument('--indexer_options', dest='indexer_options', action='store', type=str, default='')
65 options = parser.parse_args() 65 options = parser.parse_args()
66 66
67 filename = options.output 67 filename = options.output
68 68
69 params = loads( open( filename ).read() ) 69 params = loads(open(filename).read())
70 data_manager_dict = {} 70 data_manager_dict = {}
71 71
72 if options.fasta_dbkey in [ None, '', '?' ]: 72 if options.fasta_dbkey in [None, '', '?']:
73 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) 73 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (options.fasta_dbkey))
74 74
75 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) 75 sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description)
76 76
77 # build the index 77 # build the index
78 build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name ) 78 build_hisat_index(data_manager_dict, options, params, sequence_id, sequence_name)
79 79
80 # save info to json file 80 # save info to json file
81 open( filename, 'w' ).write( dumps( data_manager_dict ) ) 81 open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True))
82 82
83 83
84 if __name__ == "__main__": 84 if __name__ == "__main__":
85 main() 85 main()