Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy
view data_manager/data_manager.py @ 5:eaca3e270bf6 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 3d78021971b83d585c432830cee0488ada7bd257"
author | iuc |
---|---|
date | Fri, 19 Mar 2021 21:43:14 +0000 |
parents | cef5c909ccb8 |
children |
line wrap: on
line source
import argparse import datetime import json import os import shutil import tarfile import zipfile from urllib.request import Request, urlopen def url_download(url, workdir): file_path = os.path.join(workdir, 'download.dat') if not os.path.exists(workdir): os.makedirs(workdir) src = None dst = None try: req = Request(url) src = urlopen(req) with open(file_path, 'wb') as dst: while True: chunk = src.read(2**10) if chunk: dst.write(chunk) else: break finally: if src: src.close() if tarfile.is_tarfile(file_path): fh = tarfile.open(file_path, 'r:*') elif zipfile.is_zipfile(file_path): fh = zipfile.ZipFile(file_path, 'r') else: return fh.extractall(workdir) os.remove(file_path) def download_name_maps(url, workdir, partial): if partial: map_files = [ 'pdb.accession2taxid.gz', ] else: map_files = [ 'dead_nucl.accession2taxid.gz', 'dead_prot.accession2taxid.gz', 'dead_wgs.accession2taxid.gz', 'nucl_gb.accession2taxid.gz', 'nucl_wgs.accession2taxid.gz', 'pdb.accession2taxid.gz', 'prot.accession2taxid.gz', 'prot.accession2taxid.FULL.gz' ] if not os.path.exists(workdir): os.makedirs(workdir) for map in map_files: src = "{}{}".format(url, map) dest = os.path.join(workdir, map) print("Downloading taxonomy accession2taxid file from {} to {}".format(src, dest)) try: req = Request(src) src = urlopen(req) with open(dest, 'wb') as dst: while True: chunk = src.read(2**10) if chunk: dst.write(chunk) else: break finally: if src: src.close() def move_files_to_final_dir(workdir, target_directory, copy=False): for filename in os.listdir(workdir): if copy: shutil.copy(os.path.join(workdir, filename), target_directory) else: shutil.move(os.path.join(workdir, filename), target_directory) def main(args): workdir = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy')) url_download(args.url, workdir) data_manager_entry = {} data_manager_entry['value'] = args.name.lower() data_manager_entry['name'] = args.name data_manager_entry['path'] = '.' data_manager_json = dict(data_tables=dict(ncbi_taxonomy=data_manager_entry)) with open(args.output) as fh: params = json.load(fh) if args.name_maps: workdir_a2t = os.path.join(os.getcwd(), 'accession2taxid') download_name_maps("ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/", workdir_a2t, args.partial) target_directory_a2t = os.path.join(params['output_data'][0]['extra_files_path'], "accession2taxid") os.makedirs(target_directory_a2t) move_files_to_final_dir(workdir_a2t, target_directory_a2t) # Also copy taxonomy data to accession2taxid dir move_files_to_final_dir(workdir, target_directory_a2t, copy=True) data_manager_json['data_tables']['ncbi_accession2taxid'] = data_manager_entry target_directory_tax = os.path.join(params['output_data'][0]['extra_files_path'], "taxonomy") os.makedirs(target_directory_tax) move_files_to_final_dir(workdir, target_directory_tax) with open(args.output, 'w') as fh: json.dump(data_manager_json, fh, sort_keys=True) if __name__ == '__main__': 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=str(datetime.date.today()), help='Data table entry unique ID') parser.add_argument('--url', dest='url', action='store', default='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz', help='Download URL') parser.add_argument('--name-maps', dest='name_maps', action='store_true', help='') parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)') args = parser.parse_args() main(args)