Mercurial > repos > chrisb > gap_all_glycan_tools

comparison get_data/kegg_glycan/findKEGG.py @ 1:0a5e0df17054 draft default tip

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author chrisb
date Fri, 06 May 2016 08:05:48 -0400
parents 89592faa2875
children
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0:89592faa2875 1:0a5e0df17054
1 __author__ = 'cbarnett' 1 __author__ = 'cbarnett'
2 __license__ = "MIT" 2 __license__ = "MIT"
3 __version__ = "0.3" 3 __version__ = "0.4"
4 # http://www.kegg.jp/kegg/rest/keggapi.html 4 # http://www.kegg.jp/kegg/rest/keggapi.html
5 5
6 6
7 def find_entries_in_KEGG(db, query): 7 def find_entries_in_KEGG(db, query):
8 """ 8 """
14 14
15 if db == [] or db == "" or db is None: 15 if db == [] or db == "" or db is None:
16 raise IOError("no db given") 16 raise IOError("no db given")
17 if query == [] or query == "" or query is None: 17 if query == [] or query == "" or query is None:
18 raise IOError("no query given") 18 raise IOError("no query given")
19 query = query.replace('\n', ' ') # in case of new lines 19 query = query.replace('\n', '+') # in case of new lines, assume this means the user want to "AND"
20 query = query.replace('\r', ' ') # in case of new lines 20 query = query.replace('\r', '+') # in case of new lines, assume this means the user want to "AND"
21 query = query.replace('ec: ', 'ec:') # in case of ec: spaces - e.g. issue "ec: 2.4.99.1" spaces are ok usually as allows for combination searching "2.4.99.1 2.4.99.6"
22
23 import re
24 p = re.compile(' *\+ *') # ensure no unneccesary space in an AND query, otherwise incorrect behaviour from KEGG
25 queryfix = p.subn('+', query)
26 query=queryfix[0]
27
28 if ' ' in query:
29 query='"'+query+'"' # if spaces, query must be placed in quotes, otherwise incorrect behaviour from KEGG
30 query = query.replace(' ', '%20') # previous behaviour was ignoring text after a space, rather convert to '%20' and pass on to KEGG REST service
21 uri = 'http://rest.kegg.jp/find/' 31 uri = 'http://rest.kegg.jp/find/'
22 fulluri = uri + db + "/" + query 32 fulluri = uri + db + "/" + query
23 try: 33 try:
24 response = urllib2.urlopen(fulluri).read() 34 response = urllib2.urlopen(fulluri).read()
25 except Exception as e: 35 except Exception as e:
26 raise urllib2.HTTPError(e.url, e.code, e.msg, e.hdrs, e.fp) 36 raise urllib2.HTTPError(e.url, e.code, e.msg, e.hdrs, e.fp)
27 if str(response.strip()) == "": 37 if str(response.strip()) == "":
28 return None 38 return "" # change return from None to "" for easily writing to file
29 return response 39 return response
30 40
31 41
32 if __name__ == "__main__": 42 if __name__ == "__main__":
33 from optparse import OptionParser 43 from optparse import OptionParser