Mercurial > repos > chrisb > gap_all_glycan_tools

comparison get_data/kegg_glycan/findKEGG.py @ 0:89592faa2875 draft

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author chrisb
date Wed, 23 Mar 2016 14:35:56 -0400
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children 0a5e0df17054
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-1:000000000000 0:89592faa2875
1 __author__ = 'cbarnett'
2 __license__ = "MIT"
3 __version__ = "0.3"
4 # http://www.kegg.jp/kegg/rest/keggapi.html
5
6
7 def find_entries_in_KEGG(db, query):
8 """
9 :param db: db to search by default is glycan
10 :param query:
11 :return: string of linked entries
12 """
13 import urllib2
14
15 if db == [] or db == "" or db is None:
16 raise IOError("no db given")
17 if query == [] or query == "" or query is None:
18 raise IOError("no query given")
19 query = query.replace('\n', ' ') # in case of new lines
20 query = query.replace('\r', ' ') # in case of new lines
21 uri = 'http://rest.kegg.jp/find/'
22 fulluri = uri + db + "/" + query
23 try:
24 response = urllib2.urlopen(fulluri).read()
25 except Exception as e:
26 raise urllib2.HTTPError(e.url, e.code, e.msg, e.hdrs, e.fp)
27 if str(response.strip()) == "":
28 return None
29 return response
30
31
32 if __name__ == "__main__":
33 from optparse import OptionParser
34
35 usage = "usage: python %prog [options]\n"
36 parser = OptionParser(usage=usage)
37 parser.add_option("-d", action="store", type="string", dest="d", default="glycan",
38 help="db name, options are: pathway | brite | module | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme | disease | drug | dgroup | environ")
39 parser.add_option("-q", action="store", type="string", dest="q", default="glucose",
40 help="query e.g. glucose")
41 parser.add_option("-o", action="store", type="string", dest="o", default="found_entries.txt",
42 help="entries from search output in text format")
43 (options, args) = parser.parse_args()
44 try:
45 outstream = file(options.o, 'w')
46 except Exception as e:
47 raise IOError(e, "the output file cannot be opened. Use -h flag for help")
48 results = find_entries_in_KEGG(db=options.d, query=options.q)
49 try:
50 outstream.write(results)
51 except Exception as e:
52 raise IOError(e, "cannot open output files. -h flag for help")
53 finally:
54 outstream.close()
55
56