[Biopython-dev] WIT and KEGG

[Cayte]

----- Original Message -----
From: "Cayte" <katel at worldpath.net>
To: <tarjei at MIT.EDU>
Cc: <biopython-dev at biopython.org>
Sent: Saturday, August 11, 2001 10:52 PM
Subject: Re: [Biopython-dev] WIT and KEGG


>
> ----- Original Message -----
> From: "Tarjei S Mikkelsen" <tarjei at genome.wi.mit.edu>
> >  I'm not too fond of adding this to the format file. HTML markup isn't
> > part of the KEGG format description, so this seems a bit ad hoc.
> >
> >  Instead I suggest that you either run the input through
> > File.SGMLHandle or File.SGMLStripper before you pass the
> > WIT record to KEGG.Enzyme.Parser OR write a separate Parser
> > class in your WIT module that wraps a
ParserSupport.SGMLStrippingConsumer
> > around KEGG.Enzyme._Consumer.
> >
>   The problem is I'm experimenting with a filter to strip out junk ( not
> necessarily html ) between records.
> The motivation is that I've had Martel fail on just an extraneous line
feed.
> Somehow the idea of chaining two filters together trips a watch for bugs
> alarm in my mind.
>
> > >   The format failed halfway through the file.  I think the problem is
> the
> > > order of entries.  The format specifies GENES before MOTIF but
> > > this order is
> > > reversed in the test file.  Maybe the format should be less sensitive
to
> > > order ,where it doesn't convey information.
> >
> >  Yeah, the entries are supposed to come in a specified order, but even
> > the KEGG people don't follow that rule. I've committed a change to
> > KEGG.Enzyme.enzyme_format.py that assumes very little about entry
> > ordering. If that's the error, it should work for you now.
> >
>
> Now its stopping on files with db links like this example:
>
>             PIR: B49338  B49935  E64239  KIECAA
>
> These are quibbles but the computer doesn't understand quibbles:).
>
>                                                                  Cayte
> >  Tarjei
> >
> >
>
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