Mercurial > repos > devteam > data_manager_bwa_mem_index_builder
view data_manager/bwa_mem_index_builder.py @ 6:2a386b2383a1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
author | iuc |
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date | Mon, 18 Nov 2019 17:09:33 -0500 |
parents | 46066df8813d |
children | 63d5652be07a |
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#!/usr/bin/env python # Dan Blankenberg from __future__ import print_function import optparse import os import subprocess import sys from json import dumps, loads CHUNK_SIZE = 2**20 TWO_GB = 2**30 * 2 DEFAULT_DATA_TABLE_NAME = "bwa_mem_indexes" def get_id_name(params, dbkey, fasta_description=None): # TODO: ensure sequence_id is unique and does not already appear in location file sequence_id = params['param_dict']['sequence_id'] if not sequence_id: sequence_id = dbkey sequence_name = params['param_dict']['sequence_name'] if not sequence_name: sequence_name = fasta_description if not sequence_name: sequence_name = dbkey return sequence_id, sequence_name def build_bwa_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME): # TODO: allow multiple FASTA input files fasta_base_name = os.path.split(fasta_filename)[-1] sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name) os.symlink(fasta_filename, sym_linked_fasta_filename) if params['param_dict']['index_algorithm'] == 'automatic': if os.stat(fasta_filename).st_size < TWO_GB: # use 2 GB as cut off for memory vs. max of 2gb database size; this is somewhat arbitrary index_algorithm = 'is' else: index_algorithm = 'bwtsw' else: index_algorithm = params['param_dict']['index_algorithm'] args = ['bwa', 'index', '-a', index_algorithm] args.append(sym_linked_fasta_filename) proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) return_code = proc.wait() if return_code: print("Error building index.", file=sys.stderr) sys.exit(return_code) data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name) _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, []) data_manager_dict['data_tables'][data_table_name].append(data_table_entry) return data_manager_dict def main(): parser = optparse.OptionParser() parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename') parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey') parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description') parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name') (options, args) = parser.parse_args() filename = args[0] params = loads(open(filename).read()) target_directory = params['output_data'][0]['extra_files_path'] os.mkdir(target_directory) data_manager_dict = {} dbkey = options.fasta_dbkey if dbkey in [None, '', '?']: raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey)) sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description) # build the index build_bwa_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) # save info to json file open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True)) if __name__ == "__main__": main()