Mercurial > repos > dave > data_manager_make_blastn_dbs
view data_manager/data_manager_make_blastn_dbs.py @ 0:3da261f8ac90 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit db8f5e7fadc3bf752951b837a977919f8409e4b6-dirty
author | dave |
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date | Sat, 30 Jun 2018 16:19:53 -0400 |
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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 DEFAULT_DATA_TABLE_NAMES = ["blastn_dbs"] 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_blastn_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES): # 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) args = ['makeblastdb', '-in', sym_linked_fasta_filename, '-dbtype', "'nucl'", '-out', sequence_id] 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=sequence_id) for data_table_name in data_table_names: _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('-i', '--input', dest='input', action='store', type="string", default=None, help='Input FASTA') parser.add_option('-d', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='Unique identifier') parser.add_option('-n', '--name', dest='name', action='store', type="string", default=None, help='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 = {} 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=options.dbkey, fasta_description=options.name) # build the index build_blastn_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) # save info to json file open(filename, 'wb').write(dumps(data_manager_dict)) if __name__ == "__main__": main()