[Bioperl-l] Bioperl support for AGAVE xml

Simon K. Chan skchan at cs.usask.ca
Mon Jul 19 13:28:32 EDT 2004

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?

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...


> 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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