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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data/kegg_glycan/linkKEGG.py	Wed Mar 23 14:35:56 2016 -0400
@@ -0,0 +1,50 @@
+__author__ = 'cbarnett'
+__license__ = "MIT"
+__version = "0.3"
+# http://www.kegg.jp/kegg/rest/keggapi.html
+
+
+def linked_entries_from_kegg(targetdb="glycan", sourcedb="pathway"):
+    """
+    :param targetdb:
+    :param sourcedb:
+    :return: string  of linked entries
+    """
+    import urllib2
+
+    uri = 'http://rest.kegg.jp/link/'
+    fulluri = uri + targetdb + "/" + sourcedb
+    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 ""
+    return response
+
+
+if __name__ == "__main__":
+    from optparse import OptionParser
+
+    usage = "usage: python %prog [options]\n"
+    parser = OptionParser(usage=usage)
+    parser.add_option("-t", action="store", type="string", dest="t", default="glycan",
+                      help="target db name pathway | brite | module | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme | disease | drug | dgroup | environ")
+    parser.add_option("-s", action="store", type="string", dest="s", default="pathway",
+                      help="source db name or db entry e.g. map00010")
+    parser.add_option("-o", action="store", type="string", dest="o", default="linked_entries.txt",
+                      help="linked entries 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")
+    linked = linked_entries_from_kegg(targetdb=options.t, sourcedb=options.s)
+    try:
+        outstream.write(linked)
+    except Exception as e:
+        raise IOError(e, "cannot open output files. -h flag for help")
+    finally:
+        outstream.close()
+
+