view data_manager/mash_build_sketch.py @ 3:350da4807491 draft

planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mash_sketch/ commit 34a1400396f10e63e79511a4b28501fdaa03e77d-dirty

#!/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 = "mash_sketches"

def run(args, cwd):
    proc = subprocess.Popen(args=args, shell=False, cwd=cwd)
    return_code = proc.wait()
    if return_code:
        print("Error building sketch.", file=sys.stderr)
        sys.exit( return_code )

def mash_build_sketch(data_manager_dict, mash_args, target_directory, data_table_name=DATA_TABLE_NAME):

    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")

    database_value = "_".join([
        now,
        "refseq" + "." +
        sketch_type + "." +
        "k21.s1000.msh",
    ])

    database_name = " ".join([
        "refseq" + "." +
        sketch_type + "." +
        "k21.s1000.msh"
        "(Created:",
        now + ")"
    ])

    database_path = database_value

    args = [
        '-p', mash_args['threads'],
        '-k', mash_args['kmer_size'],
        '-s', mash_args['sketch_size'],
        '-o', 'sketch'
    ]

    subprocess.check_call(['mash', 'sketch'] + 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('--kmer-size', dest='kmer_size', help='K-mer size' )
    parser.add_argument('--sketch-size', dest='sketch_size', help='Sketch size' )
    parser.add_argument( '--threads', dest='threads', default=1, help='threads' )

    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']

    mash_args = {
        'kmer_size': args.kmer_size,
        'sketch_size': args.kmer_size,
        'threads': args.threads,
    }

    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_build_sketch(
        data_manager_output,
        mash_args,
        target_directory,
    )

    open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))


if __name__ == "__main__":
    main()