Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager/kraken2_build_database.py @ 17:4c9f9d6098eb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
author | dfornika |
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date | Mon, 06 May 2019 19:42:14 -0400 |
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children | f005b6efd096 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_database.py Mon May 06 19:42:14 2019 -0400 @@ -0,0 +1,332 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import datetime +import errno +import json +import os +import shutil +import subprocess +import sys +import tarfile +from enum import Enum + +try: + # Python3 + from urllib.request import urlopen +except ImportError: + from urllib2 import urlopen + + +DATA_TABLE_NAME = "kraken2_databases" + + +class KrakenDatabaseTypes(Enum): + standard = 'standard' + minikraken = 'minikraken' + special = 'special' + custom = 'custom' + + def __str__(self): + return self.value + + +class SpecialDatabaseTypes(Enum): + rdp = 'rdp' + greengenes = 'greengenes' + silva = 'silva' + + def __str__(self): + return self.value + + +class Minikraken2Versions(Enum): + v1 = 'v1' + v2 = 'v2' + + def __str__(self): + return self.value + + +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") + + database_value = "_".join([ + now, + "standard", + "kmer-len", str(kraken2_args["kmer_len"]), + "minimizer-len", str(kraken2_args["minimizer_len"]), + "minimizer-spaces", str(kraken2_args["minimizer_spaces"]), + ]) + + database_name = " ".join([ + "Standard", + "(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"]), + '--standard', + '--kmer-len', str(kraken2_args["kmer_len"]), + '--minimizer-len', str(kraken2_args["minimizer_len"]), + '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), + '--db', database_path + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_path + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=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 kraken2_build_minikraken(data_manager_dict, minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME): + + now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") + + database_value = "_".join([ + now, + "minikraken2", + minikraken2_version, + "8GB", + ]) + + database_name = " ".join([ + "Minikraken2", + minikraken2_version, + "(Created:", + now + ")" + ]) + + # download the minikraken2 data + src = urlopen( + 'ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_%s_8GB_201904_UPDATE.tgz' + % minikraken2_version + ) + with open('tmp_data.tar.gz', 'wb') as dst: + shutil.copyfileobj(src, dst) + # unpack the downloaded archive to the target directory + with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh: + fh.extractall(target_directory) + + data_table_entry = { + "value": database_value, + "name": database_name, + "path": database_value, + } + + _add_data_table_entry(data_manager_dict, data_table_entry) + + +def kraken2_build_special(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_database_type"], + "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_database_type"]], + "(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_database_type"], + '--kmer-len', str(kraken2_args["kmer_len"]), + '--minimizer-len', str(kraken2_args["minimizer_len"]), + '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), + '--db', database_path + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_path + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=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 kraken2_build_custom(data_manager_dict, kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME): + + args = [ + '--threads', str(kraken2_args["threads"]), + '--download-taxonomy', + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--add-to-library', kraken2_args["custom_fasta"], + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--build', + '--kmer-len', str(kraken2_args["kmer_len"]), + '--minimizer-len', str(kraken2_args["minimizer_len"]), + '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, target_directory) + + data_table_entry = { + "value": custom_database_name, + "name": custom_database_name, + "path": custom_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_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('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length') + parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length') + parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces') + parser.add_argument('--threads', dest='threads', default=1, help='threads') + parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build') + parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)') + parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)') + parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)') + parser.add_argument( '--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)' ) + 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 = {} + + print(args.database_type) + if str(args.database_type) == 'standard': + kraken2_args = { + "kmer_len": args.kmer_len, + "minimizer_len": args.minimizer_len, + "minimizer_spaces": args.minimizer_spaces, + "threads": args.threads, + } + kraken2_build_standard( + data_manager_output, + kraken2_args, + target_directory, + ) + elif str(args.database_type) == 'minikraken': + kraken2_build_minikraken( + data_manager_output, + str(args.minikraken2_version), + target_directory + ) + elif str(args.database_type) == 'special': + kraken2_args = { + "special_database_type": str(args.special_database_type), + "kmer_len": args.kmer_len, + "minimizer_len": args.minimizer_len, + "minimizer_spaces": args.minimizer_spaces, + "threads": args.threads, + } + kraken2_build_special( + data_manager_output, + kraken2_args, + target_directory, + ) + elif str(args.database_type) == 'custom': + kraken2_args = { + "custom_fasta": args.custom_fasta, + "kmer_len": args.kmer_len, + "minimizer_len": args.minimizer_len, + "minimizer_spaces": args.minimizer_spaces, + "threads": args.threads, + } + kraken2_build_custom( + data_manager_output, + kraken2_args, + args.custom_database_name, + target_directory, + ) + else: + sys.exit("Invalid database type") + + open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) + + +if __name__ == "__main__": + main()