diff get_data/glycogenedb/getglycogene_entry.py @ 0:89592faa2875 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data/glycogenedb/getglycogene_entry.py	Wed Mar 23 14:35:56 2016 -0400
@@ -0,0 +1,90 @@
+__author__ = 'cbarnett'
+__license__ = "MIT"
+
+
+def helper_get_G(lineentry):
+    if "G" in lineentry.upper():
+        splitline = lineentry.split()
+        for item in splitline:
+            if "G" in item:
+                return item
+    return None
+
+def get_acceptor_keggids(entry):
+    """
+    :param entry. entry from glycogene db
+    :return: txt keggids
+    """
+    import StringIO
+    import xml.etree.cElementTree as ET
+    #handle = StringIO.StringIO(''.join(entry))
+    handle = StringIO.StringIO(entry)
+    tree = ET.parse(handle)
+    #print tree.findtext("acceptors")
+    root = tree.getroot()
+    print root, root.tag, root.attrib
+    for elem in root.findall('./gts/acceptors/acceptor_ref'):
+        print "acceptors ", elem.tag, elem.attrib
+        a=dict(elem.attrib)
+        for key in a.keys():
+            print key, a[key]
+
+
+def get_entry_from_glycogene(gene):
+    """
+    :param gene. Gene name
+    :return: xml of entry information
+    """
+    import urllib2
+    #import xml.etree.cElementTree as ET
+
+
+    #tree = ET.parse()
+
+    uri = 'http://jcggdb.jp/rcmg/wsglycodb/ggdb/entry/'
+    #if inputstream is None or inputstream == []:
+    #    raise IOError("empty input stream")
+    gene = "ST3GAL1"
+    try: 
+        dbresponse = urllib2.urlopen(uri + gene).read()
+    except Exception as e:
+        raise urllib2.HTTPError(e.url, e.code, e.msg, e.hdrs, e.fp)
+    return dbresponse
+
+
+if __name__ == "__main__":
+    from optparse import OptionParser
+
+#    usage = "usage: python %prog [options]\n"
+#    parser = OptionParser(usage=usage)
+#    parser.add_option("-i", action="store", type="string", dest="i", default="input",
+#                      help="single or double column text file containing GL entries")
+#    parser.add_option("-k", action="store", type="string", dest="k", default="kcf.output",
+#                      help="kcf output file name")
+#    parser.add_option("-d", action="store", type="string", dest="d", default="db.output",
+#                      help="KEGG db entry in text format output file name")
+#    (options, args) = parser.parse_args()
+#    try:
+#        instream = file(options.i, 'r')
+#    except Exception as e:
+#        raise IOError(e, "the input file specified does not exist. Use -h flag for help")
+    entry =  get_entry_from_glycogene("ST3GAL1")
+    print entry
+    #instream = file("xml.xml",'r')
+    #entry = instream.read()
+    #print entry
+    get_acceptor_keggids(entry)
+    #out = file("xml.xml",'w')
+    #out.write(entry)
+    #out.close()
+#    try:
+#        kcfout = file(options.k, 'w')
+#        dbout = file(options.d, 'w')
+#    except Exception as e:
+#        raise IOError(e, "cannot open output files. -h flag for help")
+#
+#    kcfout.write("".join(kcf))
+#    dbout.write("".join(db))
+#    kcfout.close()
+#    dbout.close()
+