Mercurial > repos > dfornika > data_manager_build_mob_suite_database
view data_manager/mob_suite_build_database.py @ 7:7f67d06eeda6 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mob_suite_database/ commit ecc87b04e2f486f941c6eb4746738690db3a9e94-dirty
author | dfornika |
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date | Fri, 21 Jun 2019 20:11:10 -0400 |
parents | 34171fd6daed |
children | 12dcb412cca8 |
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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 import uuid DATA_TABLE_NAME = "mob_suite_databases" def mob_suite_build_database_mob_cluster(target_directory, mob_cluster_args, database_name, data_table_name=DATA_TABLE_NAME): now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") database_value = uuid.uuid4() database_name = database_name database_path = mob_cluster_args['outdir'] args = [ '--num_threads', mob_cluster_args['num_threads'], '--infile', mob_cluster_args['infile'], '--outdir', mob_cluster_args['outdir'], '--mode', mob_cluster_args['mode'], ] subprocess.check_call(['mob_cluster'] + args, cwd=target_directory) data_table_entry = { "data_tables": { data_table_name: [ { "value": database_value, "name": database_name, "path": database_path, } ] } } return data_table_entry def main(): parser = argparse.ArgumentParser() parser.add_argument('data_manager_json') parser.add_argument('--threads', dest='threads', default=1, help='threads') parser.add_argument('--input', dest='input', help='Plasmid Assemblies (.fasta)') parser.add_argument('--database-name', dest='database_name', help='Database Name') args = parser.parse_args() 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 = {} mob_cluster_args = { 'num_threads': args.threads, 'infile': args.input, 'mode': 'build', 'outdir': 'out', } data_manager_output = mob_suite_build_database_mob_cluster( target_directory, mob_cluster_args, args.database_name, ) open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) if __name__ == "__main__": main()