[Biopython-dev] [Bug 2403] prosite parser can't handle new PROSITE/PRORULE format

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2403





------- Comment #9 from biopython-bugzilla at maubp.freeserve.co.uk  2007-11-20 08:39 EST -------
Issue Two:

The PP lines problem should be  fixed with with Bio/Prosite/__init__.py CVS
revision 1.15

Your patch was pretty close, you seem to have more or less understood how this
parser works :)

One problem I did notice was:

+    def _scan_pp(self, uhandle, consumer):
+        #New PP line, PostProcessing
+        self._scan_line('PP', uhandle, consumer.prorule, any_number=1)

Should have been:

+    def _scan_pp(self, uhandle, consumer):
+        #New PP line, PostProcessing
+        self._scan_line('PP', uhandle, consumer.postprocessing, any_number=1)

Otherwise any PP lines would get treated like PR lines!

Could you get the latest code, and confirm this works prosite.dat (version 20)?
 There may be other quirks as I have only tried a few ProSite files myself... 

Thank you, Peter.


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