Mercurial > repos > dfornika > data_manager_mash_sketch_builder
diff data_manager/mash_sketch_builder.py @ 0:647eedfd1556 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
author | dfornika |
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date | Sat, 22 Feb 2020 00:30:35 +0000 |
parents | |
children | af86557c1b87 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/mash_sketch_builder.py Sat Feb 22 00:30:35 2020 +0000 @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +import argparse +import errno +import json +import os +import subprocess +import sys + + +DATA_TABLE_NAME = "mash_sketches" + + +def mash_sketch(mash_sketch_args, sketch_name, target_directory, data_table_name=DATA_TABLE_NAME): + UUID = str(uuid.uuid4()) + + os.mkdir(os.path.join(target_directory, UUID)) + + sketch_path = os.path.join(UUID, "sketch"), + + args = [ + '--threads', str(kraken2_args["threads"]), + '-k', str(mash_sketch_args["kmer_size"]), + '-s', str(mash_sketch_args["sketch_size"]), + '-o', sketch_path + ] + + subprocess.check_call(['mash', 'sketch'] + args, cwd=target_directory) + + if kraken2_args["clean"]: + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_path + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + data_table_entry = { + 'data_tables': { + data_table_name: [ + { + "value": UUID, + "name": sketch_name, + "path": sketch_path, + } + ] + } + } + + return data_table_entry + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('data_manager_json') + parser.add_argument('--kmer-size', dest='kmer_size', type=int, default=35, help='kmer length') + parser.add_argument('--sketch-size', dest='sketch_size', type=int, default=31, help='minimizer length') + parser.add_argument('--threads', dest='threads', default=1, help='threads') + parser.add_argument('--sketch-name', dest='sketch_name', help='Name for sketch') + 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 = {} + + mash_sketch_args = { + "kmer_size": args.kmer_len, + "sketch_size": args.minimizer_len, + "threads": args.threads, + } + + open(args.data_manager_json, 'w').write(json.dumps(data_manager_output, sort_keys=True)) + + +if __name__ == "__main__": + main()