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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data/kegg_glycan/findKEGG.py	Wed Mar 23 14:35:56 2016 -0400
@@ -0,0 +1,56 @@
+__author__ = 'cbarnett'
+__license__ = "MIT"
+__version__ = "0.3"
+# http://www.kegg.jp/kegg/rest/keggapi.html
+
+
+def find_entries_in_KEGG(db, query):
+    """
+    :param db: db to search by default is glycan
+    :param query:
+    :return: string  of linked entries
+    """
+    import urllib2
+
+    if db == [] or db == "" or db is None:
+        raise IOError("no db given")
+    if query == [] or query == "" or query is None:
+        raise IOError("no query given")
+    query = query.replace('\n', ' ')  # in case of new lines
+    query = query.replace('\r', ' ')  # in case of new lines
+    uri = 'http://rest.kegg.jp/find/'
+    fulluri = uri + db + "/" + query
+    try:
+        response = urllib2.urlopen(fulluri).read()
+    except Exception as e:
+        raise urllib2.HTTPError(e.url, e.code, e.msg, e.hdrs, e.fp)
+    if str(response.strip()) == "":
+        return None
+    return response
+
+
+if __name__ == "__main__":
+    from optparse import OptionParser
+
+    usage = "usage: python %prog [options]\n"
+    parser = OptionParser(usage=usage)
+    parser.add_option("-d", action="store", type="string", dest="d", default="glycan",
+                      help="db name, options are: pathway | brite | module | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme | disease | drug | dgroup | environ")
+    parser.add_option("-q", action="store", type="string", dest="q", default="glucose",
+                      help="query e.g. glucose")
+    parser.add_option("-o", action="store", type="string", dest="o", default="found_entries.txt",
+                      help="entries from search output in text format")
+    (options, args) = parser.parse_args()
+    try:
+        outstream = file(options.o, 'w')
+    except Exception as e:
+        raise IOError(e, "the output file cannot be opened. Use -h flag for help")
+    results = find_entries_in_KEGG(db=options.d, query=options.q)
+    try:
+        outstream.write(results)
+    except Exception as e:
+        raise IOError(e, "cannot open output files. -h flag for help")
+    finally:
+        outstream.close()
+
+