[BioPython] Prosite / Prorule

[Michiel De Hoon]

Holger wrote:
> 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 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'
...
> Is the parsing mechanism described anywhere, so I can look it up and fix
the error?

The Prosite parser was written about five years ago, and it may very well be
that none of the currently active Biopython developers really know how this
parser works. In that case, one option may be to write a new Prosite parser
from scratch. That could even be an easier solution than trying to fix the
existing parser. If you decide to go that way, it would be a good idea to
discuss the Prosite parser design beforehand on the development mailing list
(biopython-dev at biopython.org).

--Michiel


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032