Mercurial > repos > devteam > data_manager_bowtie2_index_builder

comparison data_manager/bowtie2_index_builder.py @ 7:1c0f8e9d87c6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 9fa01fe96452d50646e066066b1e556ba4a75ced"
author iuc
date Mon, 06 Apr 2020 19:27:05 -0400
parents d1d5feb31804
children 1586b111d2a3
comparison
equal deleted inserted replaced
6:847c9ef56a52 7:1c0f8e9d87c6
9 from json import dumps, loads 9 from json import dumps, loads
10 10
11 DEFAULT_DATA_TABLE_NAMES = ["bowtie2_indexes"] 11 DEFAULT_DATA_TABLE_NAMES = ["bowtie2_indexes"]
12 12
13 13
14 def get_id_name( params, dbkey, fasta_description=None): 14 def get_id_name(params, dbkey, fasta_description=None):
15 # TODO: ensure sequence_id is unique and does not already appear in location file 15 # TODO: ensure sequence_id is unique and does not already appear in location file
16 sequence_id = params['param_dict']['sequence_id'] 16 sequence_id = params['param_dict']['sequence_id']
17 if not sequence_id: 17 if not sequence_id:
18 sequence_id = dbkey 18 sequence_id = dbkey
19 19
23 if not sequence_name: 23 if not sequence_name:
24 sequence_name = dbkey 24 sequence_name = dbkey
25 return sequence_id, sequence_name 25 return sequence_id, sequence_name
26 26
27 27
28 def build_bowtie2_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES ): 28 def build_bowtie2_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES):
29 # TODO: allow multiple FASTA input files 29 # TODO: allow multiple FASTA input files
30 fasta_base_name = os.path.split( fasta_filename )[-1] 30 fasta_base_name = os.path.split(fasta_filename)[-1]
31 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) 31 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
32 os.symlink( fasta_filename, sym_linked_fasta_filename ) 32 os.symlink(fasta_filename, sym_linked_fasta_filename)
33 args = [ 'bowtie2-build', sym_linked_fasta_filename, sequence_id ] 33 args = ['bowtie2-build', sym_linked_fasta_filename, sequence_id]
34 threads = os.environ.get('GALAXY_SLOTS') 34 threads = os.environ.get('GALAXY_SLOTS')
35 if threads: 35 if threads:
36 args.extend(['--threads', threads]) 36 args.extend(['--threads', threads])
37 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) 37 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
38 return_code = proc.wait() 38 return_code = proc.wait()
39 if return_code: 39 if return_code:
40 print("Error building index.", file=sys.stderr) 40 print("Error building index.", file=sys.stderr)
41 sys.exit( return_code ) 41 sys.exit(return_code)
42 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id ) 42 data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id)
43 for data_table_name in data_table_names: 43 for data_table_name in data_table_names:
44 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) 44 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
45 45
46 46
47 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): 47 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
48 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 48 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
49 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) 49 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
50 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) 50 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
51 return data_manager_dict 51 return data_manager_dict
52 52
53 53
54 def main(): 54 def main():
55 parser = optparse.OptionParser() 55 parser = optparse.OptionParser()
56 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) 56 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
57 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) 57 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
58 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) 58 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
59 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='append', type="string", default=None, help='data_table_name' ) 59 parser.add_option('-n', '--data_table_name', dest='data_table_name', action='append', type="string", default=None, help='data_table_name')
60 (options, args) = parser.parse_args() 60 (options, args) = parser.parse_args()
61 61
62 filename = args[0] 62 filename = args[0]
63 63
64 params = loads( open( filename ).read() ) 64 params = loads(open(filename).read())
65 target_directory = params[ 'output_data' ][0]['extra_files_path'] 65 target_directory = params['output_data'][0]['extra_files_path']
66 os.mkdir( target_directory ) 66 os.mkdir(target_directory)
67 data_manager_dict = {} 67 data_manager_dict = {}
68 68
69 dbkey = options.fasta_dbkey 69 dbkey = options.fasta_dbkey
70 70
71 if dbkey in [ None, '', '?' ]: 71 if dbkey in [None, '', '?']:
72 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) 72 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
73 73
74 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description ) 74 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
75 75
76 # build the index 76 # build the index
77 build_bowtie2_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES ) 77 build_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES)
78 78
79 # save info to json file 79 # save info to json file
80 with open(filename, 'w') as json_out: 80 with open(filename, 'w') as json_out:
81 json_out.write( dumps( data_manager_dict, sort_keys=True ) ) 81 json_out.write(dumps(data_manager_dict, sort_keys=True))
82 82
83 83
84 if __name__ == "__main__": 84 if __name__ == "__main__":
85 main() 85 main()