[Bioperl-l] Bioperl support for AGAVE xml

[Jason Stajich]

On Mon, 19 Jul 2004, Simon K. Chan wrote:

> Hi Brian,
>
>
> > Yes, there's this stray sentence. "Several of these have been proposed and
> > bioperl has at least some support for three: GAME, BSML and AGAVE." I'm not
> > sure what was meant by the word "some" at that time but my guess would be
> > that 1.4 has no support for AGAVE.
>
> Ok, thanks for clearing that up.  Should we update that sentence then?
>
> > Would you like to see agave.pm put into
> > Bioperl? If your agave.pm is functional then this is just a matter of adding
> > it and writing a test script. What XML parser does it use?
>
>
> At the moment, I'm using regexps to parse the XML (similar to the tigr.pm
> module).  I noticed that game.pm uses XML::Parser::PerlSAX.  Should I use this
> one instead of the regexps?
>

I would argue we should be aiming to use XML::SAX in the future - it can
use various different modules including XML::Parser::PerlSAX as back-ends.

We should NOT be using XML::DOM anymore and it would be nice to change the
BSML parser over to using a SAX model at some point.  You can see an
example of XML::SAX in action in my Bio::SeqIO::tigrxml which is just in
CVS.


> Yes, I'd like agave.pm added to CVS so I can commit changes/additions as they
> come up.
>
> Let me know if you have any other comments/suggestions...
>
> Thanks.
>
>
>
> > Brian O.
> >
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at portal.open-bio.org
> > [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Simon K. Chan
> > Sent: Monday, July 19, 2004 12:32 PM
> > To: bioperl-l at bioperl.org
> > Subject: [Bioperl-l] Bioperl support for AGAVE xml
> >
> > Hi,
> >
> > Is there currently any support for the AGAVE xml format in bioperl?
> >
> > Section III.7.7 of the bptutorial specifies that there is some support for
> > AGAVE, but I have been unable to locate this support.
> >
> > There is a Bio::SeqIO::agave.pm module located here
> > http://www.lifecde.com/products/agave/agave.pm
> >
> > According to the bioperl/biojava mailing list archives, the above code was
> > submitted to the lists for comments/suggestions in 2001, but it appears that
> > nothing much has happened since.
> >
> > I have modified some of the methods in the module to suit my needs, but
> > would
> > like to know what else is out there in terms of bioperl support.
> >
> > Many thanks for any comments/suggestions.
> >
> > Cheers,
> >
> >
> > --
> > Warmest Regards,
> > Simon K. Chan
> > Bioinformatics, Crosby Lab
> > skchan at cs.usask.ca
> >
> >
> >
> >
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> >
> >
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu