Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager/kraken2_build_standard.py @ 0:7e43f66abe9d draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
author | dfornika |
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date | Thu, 28 Feb 2019 02:32:38 -0500 |
parents | |
children | 32d04371ed19 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_standard.py Thu Feb 28 02:32:38 2019 -0500 @@ -0,0 +1,96 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import datetime +import errno +import json +import os +import string +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): + today = datetime.date.today().isoformat() + database_name = "_".join([today, "standard"]) + args = [ + 'kraken2-build', + '--threads', str(kraken2_args["threads"]), + '--standard', + '--kmer-len', str(kraken2_args["kmer_len"]), + '--minimizer-len', str(kraken2_args["minimizer_len"]), + '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), + '--db', database_name + ] + pprint(args) + 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 ) + + 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) + + +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 = argparse.ArgumentParser() + parser.add_argument('params') + 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' ) + parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' ) + args = parser.parse_args() + + kraken2_args = { + "kmer_len": args.kmer_len, + "minimizer_len": args.minimizer_len, + "minimizer_spaces": args.minimizer_spaces, + "threads": args.threads, + } + + params = json.loads(open(args.params).read()) + pprint(params) + target_directory = params['output_data'][0]['extra_files_path'] + + try: + os.mkdir( target_directory ) + except OSError as exc: + if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): + pass + else: + raise + + data_manager_dict = {} + + # build the index + kraken2_build_standard( + data_manager_dict, + kraken2_args, + params, + target_directory + ) + + # save info to json file + open(args.params, 'wb').write(json.dumps(data_manager_dict)) + + +if __name__ == "__main__": + main()