annotate data_manager/bwameth_index_builder.py @ 6:fca923910aaa draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

#!/usr/bin/env python
# Based heavily on the HISAT2 data manager wrapper

import argparse
import json
import os
import subprocess
import sys

DEFAULT_DATA_TABLE_NAME = "bwameth_indexes"


def build_bwameth_index(data_manager_dict, params, args):
    data_table_name = args.data_table_name
    target_directory = params['output_data'][0]['extra_files_path']
    if not os.path.exists(target_directory):
        os.mkdir(target_directory)
    fasta_base_name = os.path.basename(args.fasta_filename)
    sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
    os.symlink(os.path.abspath(args.fasta_filename), sym_linked_fasta_filename)
    cmd = ['bwameth.py', 'index', sym_linked_fasta_filename]
    proc = subprocess.Popen(args=cmd, shell=False, cwd=target_directory)
    return_code = proc.wait()
    if return_code:
        print("Error building index.", file=sys.stderr)
        sys.exit(return_code)
    data_table_entry = dict(value=args.dbkey, dbkey=args.dbkey, name=args.name, path=sym_linked_fasta_filename)
    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)


def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
    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():
    # Parse Command Line
    parser = argparse.ArgumentParser()
    parser.add_argument('--output', default=None)
    parser.add_argument('--fasta_filename', default=None)
    parser.add_argument('--dbkey', default=None)
    parser.add_argument('--name', default=None)
    parser.add_argument('--description', default=None)
    parser.add_argument('--data_table_name', default=DEFAULT_DATA_TABLE_NAME)
    args = parser.parse_args()

    filename = args.output
    with open(filename) as fh:
        params = json.load(fh)
    data_manager_dict = {}

    if args.dbkey in [None, '', '?']:
        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey))

    # build the index
    build_bwameth_index(data_manager_dict, params, args)

    # save info to json file
    with open(filename, 'w') as fh:
        json.dump(data_manager_dict, fh, sort_keys=True)


if __name__ == "__main__":
    main()