Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation

comparison data_manager_gene_annotation/data_manager/data_manager.py @ 0:0442068f5c91 draft

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author scottx611x
date Tue, 26 Apr 2016 13:33:16 -0400
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children 810ef478fc98
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-1:000000000000 0:0442068f5c91
1 import argparse
2 import datetime
3 import json
4 import os
5 import shutil
6 import sys
7 import tarfile
8 import urllib2
9 import zipfile
10
11 parser = argparse.ArgumentParser(description='Create data manager json.')
12 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
13 parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID')
14 parser.add_argument('--url', dest='url', action='store', help='Download URL', default="http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf")
15
16 args = parser.parse_args()
17
18 def url_download(url, workdir):
19 if not os.path.exists(workdir):
20 os.makedirs(workdir)
21 file_path = os.path.join(workdir, 'download.dat')
22 if not os.path.exists(workdir):
23 os.makedirs(workdir)
24 src = None
25 dst = None
26 hdr = {'User-Agent': 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.64 Safari/537.11',
27 'Accept': 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8',
28 'Accept-Charset': 'ISO-8859-1,utf-8;q=0.7,*;q=0.3',
29 'Accept-Encoding': 'none',
30 'Accept-Language': 'en-US,en;q=0.8',
31 'Connection': 'keep-alive'}
32 try:
33 req = urllib2.Request(url, headers=hdr)
34 src = urllib2.urlopen(req)
35 dst = open(file_path, 'wb')
36 while True:
37 chunk = src.read(2**10)
38 if chunk:
39 dst.write(chunk)
40 else:
41 break
42 except Exception as e:
43 print e, "FUCK"
44 finally:
45 if src:
46 src.close()
47 if dst:
48 dst.close()
49 if tarfile.is_tarfile(file_path):
50 fh = tarfile.open(file_path, 'r:*')
51 elif zipfile.is_zipfile(file_path):
52 fh = zipfile.ZipFile(file_path, 'r')
53 else:
54 return
55 fh.extractall(workdir)
56 os.remove(file_path)
57
58
59 def main(args):
60 workdir = os.path.join(os.getcwd(), 'gene_annotation')
61 url_download(args.url, workdir)
62 data_manager_entry = {}
63 data_manager_entry['value'] = args.name.lower()
64 data_manager_entry['name'] = args.name
65 data_manager_entry['path'] = args.output
66 data_manager_json = dict(data_tables=dict(gene_annotation=data_manager_entry))
67 params = json.loads(open(args.output).read())
68 target_directory = params['output_data'][0]['extra_files_path']
69 os.mkdir(target_directory)
70 output_path = os.path.abspath(os.path.join(os.getcwd(), 'gene_annotation'))
71 for filename in os.listdir(workdir):
72 shutil.move(os.path.join(output_path, filename), target_directory)
73 file(args.output, 'w').write(json.dumps(data_manager_json))
74
75 if __name__ == '__main__':
76 main(args)