Mercurial > repos > xuebing > sharplabtool

comparison tools/data_source/ucsc_proxy.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2 import urllib
3 import sys, os
4
5 assert sys.version_info[:2] >= ( 2, 4 )
6
7 CHUNK = 2**20 # 1Mb
8 MAXSIZE = CHUNK * 100
9 if __name__ == '__main__':
10
11 if len(sys.argv) != 3:
12 print 'Usage ucsc.py input_params output_file'
13 sys.exit()
14
15 inp_file = sys.argv[1]
16 out_file = sys.argv[2]
17
18 DEFAULT_URL = "http://genome.ucsc.edu/hgTables?"
19
20 # this must stay a list to allow multiple selections for the same widget name (checkboxes)
21 params = []
22 for line in file(inp_file):
23 line = line.strip()
24 if line:
25 parts = line.split('=')
26 if len(parts) == 0:
27 key = ""
28 value = ""
29 elif len(parts) == 1:
30 key = parts[0]
31 value = ""
32 else:
33 key = parts[0]
34 value = parts[1]
35 if key == 'display':
36 print value
37 # get url from params, refered from proxy.py, initialized by the tool xml
38 elif key == 'proxy_url':
39 DEFAULT_URL = value
40 else:
41 params.append( (key, value) )
42
43 #print params
44
45 encoded_params = urllib.urlencode(params)
46 url = DEFAULT_URL + encoded_params
47
48 #print url
49
50 page = urllib.urlopen(url)
51
52 fp = open(out_file, 'wt')
53 size = 0
54 while 1:
55 data = page.read(CHUNK)
56 if not data:
57 break
58 if size > MAXSIZE:
59 fp.write('----- maximum datasize exceeded ---\n')
60 break
61 size += len(data)
62 fp.write(data)
63
64 fp.close()
65