Mercurial > repos > chrisw > data_manager_monorail_index_fetcher
view data_manager_monorail_index/data_manager/data_manager.py @ 10:7d7328ce424b draft
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author | chrisw |
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date | Wed, 13 Nov 2019 21:02:28 +0000 |
parents | 79f33bace3da |
children | 11daa95fdc3e |
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#based off of "Gene Annotation Fetcher" https://testtoolshed.g2.bx.psu.edu/repository?repository_id=c0f5466df187cc04&changeset_revision=444300ec9185 import argparse import datetime import json import os import shutil import sys import tarfile import urllib2 import zipfile parser = argparse.ArgumentParser(description='Create data manager json.') parser.add_argument('--out', dest='output', action='store', help='JSON filename') parser.add_argument('--name', dest='name', action='store', default=None, help='Data table entry unique ID') parser.add_argument('--url', dest='url', action='store', help='Monorail Indexes Base URL', default="http://snaptron.cs.jhu.edu/data/monorail/ath10") args = parser.parse_args() def main(args): workdir = os.path.join(os.getcwd(), 'monorail_index') data_manager_entry = {} ref = args.url.split('/')[-1] data_manager_entry['dbkey'] = 'mrail.'+ref data_manager_entry['value'] = ref.lower() jsonin = open(args.output).read() params = json.loads(jsonin) target_directory = params['output_data'][0]['extra_files_path'] #data_manager_entry['path'] = params['output_data'][0]['extra_files_path'] data_manager_entry['path'] = target_directory data_manager_entry['name'] = ref #data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + 'gtf' + os.sep + 'exons.bed' data_manager_json = dict(data_tables={'monorail_index': [data_manager_entry]}) file(args.output, 'wb').write(json.dumps(data_manager_json)) if __name__ == '__main__': main(args)