Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager/kraken2_build_standard.py @ 5:1f6fe9dc5490 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
author | dfornika |
---|---|
date | Mon, 04 Mar 2019 18:59:44 -0500 |
parents | 32d04371ed19 |
children | ae6180bdb1e9 |
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--- a/data_manager/kraken2_build_standard.py Fri Mar 01 14:01:57 2019 -0500 +++ b/data_manager/kraken2_build_standard.py Mon Mar 04 18:59:44 2019 -0500 @@ -11,15 +11,26 @@ import subprocess import sys -from pprint import pprint DATA_TABLE_NAME = "kraken2_databases" -def kraken2_build_standard(data_manager_dict, kraken2_args, params, target_directory, data_table_name=DATA_TABLE_NAME): +def run(args, cwd): + proc = subprocess.Popen(args=args, shell=False, cwd=cwd) + return_code = proc.wait() + if return_code: + print("Error building database.", file=sys.stderr) + sys.exit( return_code ) + +def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): today = datetime.date.today().isoformat() - database_name = "_".join([today, "standard"]) + database_name = "_".join([ + today, + "standard", + "kmer-len=" + str(kraken2_args["kmer_len"]), + "minimizer-len=" + str(kraken2_args["minimizer_len"]), + "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]), + ]) args = [ - 'kraken2-build', '--threads', str(kraken2_args["threads"]), '--standard', '--kmer-len', str(kraken2_args["kmer_len"]), @@ -27,41 +38,37 @@ '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), '--db', database_name ] - proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) - return_code = proc.wait() - if return_code: - print("Error building database.", file=sys.stderr) - sys.exit( return_code ) + + run(['kraken2-build'] + args, target_directory) + args = [ 'kraken2-build', '--threads', str(kraken2_args["threads"]), '--clean', '--db', database_name ] - proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) - return_code = proc.wait() - if return_code: - print("Error building database.", file=sys.stderr) - sys.exit( return_code ) + + run(['kraken2-build'] + args, target_directory) + data_table_entry = { "value": database_name, "name": database_name, "path": database_name } - _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) + _add_data_table_entry(data_manager_dict, data_table_entry) -def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): +def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME): 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 ) + 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 = argparse.ArgumentParser() - parser.add_argument('params') + parser.add_argument('data_manager_json') parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' ) parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' ) parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' ) @@ -75,9 +82,9 @@ "threads": args.threads, } - params = json.loads(open(args.params).read()) - pprint(params) - target_directory = params['output_data'][0]['extra_files_path'] + data_manager_input = json.loads(open(args.data_manager_json).read()) + + target_directory = data_manager_input['output_data'][0]['extra_files_path'] try: os.mkdir( target_directory ) @@ -87,18 +94,13 @@ else: raise - data_manager_dict = {} - - # build the index kraken2_build_standard( - data_manager_dict, + data_manager_input, kraken2_args, - params, - target_directory + target_directory, ) - # save info to json file - open(args.params, 'wb').write(json.dumps(data_manager_dict)) + open(args.data_manager_json, 'wb').write(json.dumps(data_manager_input)) if __name__ == "__main__":