view data_manager/fetch_artic_primers.py @ 3:6114f017f819 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"

#!/usr/bin/env python

from __future__ import print_function, division

import argparse
import json
import os
import os.path
import sys

import requests

DATA_TABLE_NAME = 'artic_primers'
def fetch_artic_primers(output_filename, output_directory, primers):
    primer_sets = {
        'ARTICv1': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed',
        'ARTICv2': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed',
        'ARTICv3': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed'
        }

    if not os.path.isdir(output_directory):
        os.makedirs(output_directory)
    data_manager_dict = {}
    data_manager_dict['data_tables'] = json.load(open(output_filename)).get('data_tables', {})
    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 = []
    for name, url in primer_sets.items():
        if name not in primers:
            continue
        response = requests.get(url)
        if response.status_code != 200:
            print('Error: download of', url, 'failed with code', response.status_code, file=sys.stderr)
            exit(response.status_code)
        bed_output_filename = os.path.join(output_directory, name + '.bed')
        open(bed_output_filename, 'w').write(response.text)
        description = name[:-2] + ' ' + name[-2:] + ' primer set'
        data.append(dict(value=name, path=bed_output_filename, description=description))
    data_manager_dict['data_tables'][DATA_TABLE_NAME].extend(data)
    print(data_manager_dict)
    json.dump(data_manager_dict, open(output_filename, 'w'))

class SplitArgs(argparse.Action):
    def __call__(self, parser, namespace, values, option_string=None):
        setattr(namespace, self.dest, values.split(','))

                
if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Fetch ARTIC primer files for Galaxy use')
    parser.add_argument('--output_directory', default='tmp', help='Directory to write output to')
    parser.add_argument('--galaxy_datamanager_filename', help='Galaxy JSON format file describing data manager inputs')
    parser.add_argument('--primers', default='ARTCIv1,ARTICv2,ARTICv3', action=SplitArgs, help='Comma separated list of primers to fetch')
    args = parser.parse_args()
    
    config = json.load(open(args.galaxy_datamanager_filename))
    output_directory = config.get('output_data', [{}])[0].get('extra_files_path', None)
    if output_directory is None:
        output_directory = args.output_directory
    fetch_artic_primers(args.galaxy_datamanager_filename, output_directory, args.primers)