Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
view data_manager_gene_annotation/data_manager/data_manager.py @ 43:e42284a13168 draft
planemo upload
author | scottx611x |
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date | Fri, 08 Jul 2016 14:45:18 -0400 |
parents | bf05cda04e1f |
children | f8cfca91827a |
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import os import sys import json import argparse import requests from requests.exceptions import ContentDecodingError def url_download(url): """Attempt to download gene annotation file from a given url :param url: full url to gene annotation file :type url: str. :returns: name of downloaded gene annotation file :raises: ContentDecodingError, IOError """ response = requests.get(url=url, stream=True) # Generate file_name file_name = response.url.split("/")[-1] block_size = 10 * 1024 * 1024 # 10MB chunked download with open(file_name, 'w+') as f: try: # Good to note here that requests' iter_content() will # automatically handle decoding "gzip" and "deflate" encoding # formats for buf in response.iter_content(block_size): f.write(buf) except (ContentDecodingError, IOError) as e: sys.stderr.write("Error occured downloading reference file: %s" % e) os.remove(file_name) return file_name def main(): # Generate and parse command line args 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='Url to download gtf file from') args = parser.parse_args() work_dir = os.getcwd() # Attempt to download gene annotation file from given url gene_annotation_file_name = url_download(args.url) name = str(args.name) if not name: name = gene_annotation_file_name.split(".")[0] # Update Data Manager JSON and write to file data_manager_entry = { 'data_tables': { 'gene_annotation': { 'value': gene_annotation_file_name.split(".")[0], 'dbkey': gene_annotation_file_name.split(".")[0], 'name': name, 'path': gene_annotation_file_name } } } with open(os.path.join(args.output), "w+") as f: f.write(json.dumps(data_manager_entry)) if __name__ == '__main__': main()