Mercurial > repos > dfornika > data_manager_build_kraken2_database
view data_manager/kraken2_build_special.py @ 12:039a65ff445d draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author | dfornika |
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date | Tue, 05 Mar 2019 15:11:05 -0500 |
parents | 1dc93ae264e6 |
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#!/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 DATA_TABLE_NAME = "kraken2_databases" 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): now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") special_database_names = { "rdp": "RDP", "greengenes": "Greengenes", "silva": "Silva", } database_value = "_".join([ now, kraken2_args["special"], "kmer-len", str(kraken2_args["kmer_len"]), "minimizer-len", str(kraken2_args["minimizer_len"]), "minimizer-spaces", str(kraken2_args["minimizer_spaces"]), ]) database_name = " ".join([ special_database_names[kraken2_args["special"]], "(Created:", now + ",", "kmer-len=" + str(kraken2_args["kmer_len"]) + ",", "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",", "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")", ]) database_path = database_value args = [ '--threads', str(kraken2_args["threads"]), '--special', kraken2_args["special"], '--kmer-len', str(kraken2_args["kmer_len"]), '--minimizer-len', str(kraken2_args["minimizer_len"]), '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), '--db', database_path ] run(['kraken2-build'] + args, target_directory) args = [ '--threads', str(kraken2_args["threads"]), '--clean', '--db', database_path ] run(['kraken2-build'] + args, target_directory) data_table_entry = { "value": database_value, "name": database_name, "path": database_path, } _add_data_table_entry(data_manager_dict, 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 ) return data_manager_dict def main(): parser = argparse.ArgumentParser() parser.add_argument('data_manager_json') parser.add_argument( '-b', '--db-type', dest='db_type', help='database type (one of: silva, rdp, greengenes)' ) 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 = { "special": args.db_type, "kmer_len": args.kmer_len, "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, } 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 ) except OSError as exc: if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): pass else: raise data_manager_output = {} kraken2_build_standard( data_manager_output, kraken2_args, target_directory, ) open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) if __name__ == "__main__": main()