[BioPython] Prosite / Prorule
Peter
biopython at maubp.freeserve.co.uk
Fri Nov 16 16:02:12 UTC 2007
holger.dinkel at gmail.com wrote:
> Hello List,
>
> I just stumbled upon an error with the parsing of a 'newer' (>20) version of
> Prosite: Prosite introduced a new field called ProRules which cause errors
> in parsing with Bio/Prosite/__init__.py / Bio/ParserSupport.py.
> I updated biopython to 1.44, but the error persists.
Could you file a bug and attach a small recent Prosite file which has
this problem?
> I tried to figure out, where the problem lies, but I do not really understand
> the structure of the parsing modules in 'Bio/Prosite/__init__.py'
> I tried to create a new entry for the prorule:
> define a
>
> def _scan_pr(self, uhandle, consumer):
> self._scan_line('PR', uhandle, consumer.identification, up_to_one=1)
>
> add that to the '_scan_fns' and so on, but then the scanning order seems to get
> out of order, and i get a different "SyntaxError: Line does not start with ..."
> error...
Note that the order in _scan_fns does matter.
> Is the parsing mechanism described anywhere, so I can look it up and fix the error?
Not that I am aware of, however the SwissProt parser looks very similar,
so we should be able to fix this without too much hassle.
Thanks
Peter
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