annotate get_data/kegg_glycan/linkKEGG.py @ 1:0a5e0df17054 draft default tip

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1 __author__ = 'cbarnett'
2 __license__ = "MIT"
3 __version = "0.3.1"
4 # http://www.kegg.jp/kegg/rest/keggapi.html
5 
6 
7 def linked_entries_from_kegg(targetdb="glycan", sourcedb="pathway"):
8     """
9     :param targetdb:
10     :param sourcedb:
11     :return: string  of linked entries
12     """
13     import urllib2
14 
15     uri = 'http://rest.kegg.jp/link/'
16 
17     import re
18     p = re.compile(' *\+ *') # ensure no unneccessary space in an AND query
19     sdbfix = p.subn('+', sourcedb)
20     sourcedb=sdbfix[0]
21 
22     if ' ' in sourcedb:
23         sourcedb = sourcedb.replace(' ', '%20')  # previous behaviour was ignoring text after a space, rather convert to '%20' and pass on to KEGG REST service
24 
25     fulluri = uri + targetdb + "/" + sourcedb
26     try:
27         response = urllib2.urlopen(fulluri).read()
28     except Exception as e:
29         raise urllib2.HTTPError(e.url, e.code, e.msg, e.hdrs, e.fp)
30     if str(response.strip()) == "":
31         return ""
32     return response
33 
34 
35 if __name__ == "__main__":
36     from optparse import OptionParser
37 
38     usage = "usage: python %prog [options]\n"
39     parser = OptionParser(usage=usage)
40     parser.add_option("-t", action="store", type="string", dest="t", default="glycan",
41                       help="target db name pathway | brite | module | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme | disease | drug | dgroup | environ")
42     parser.add_option("-s", action="store", type="string", dest="s", default="pathway",
43                       help="source db name or db entry e.g. map00010")
44     parser.add_option("-o", action="store", type="string", dest="o", default="linked_entries.txt",
45                       help="linked entries output in text format")
46     (options, args) = parser.parse_args()
47     try:
48         outstream = file(options.o, 'w')
49     except Exception as e:
50         raise IOError(e, "the output file cannot be opened. Use -h flag for help")
51     linked = linked_entries_from_kegg(targetdb=options.t, sourcedb=options.s)
52     try:
53         outstream.write(linked)
54     except Exception as e:
55         raise IOError(e, "cannot open output files. -h flag for help")
56     finally:
57         outstream.close()
58 
59