[Bioperl-l] Bioperl support for AGAVE xml

[Simon K. Chan]

Hi,

Ok, Jason.  XML::SAX it is!

Brian,
No, I don't have my own bioperl cvs account.  If I could get one, that would be
great because I definately will be continously working on agave.pm (and
possibly other modules).

Let me know the details.

Many thanks, All.

Cheers,
--
Warmest Regards,
Simon K. Chan
Bioinformatics, Crosby Lab
skchan at cs.usask.ca


Quoting Brian Osborne <brian_osborne at cognia.com>:

> Simon,
>
> I'll fix the documentation in various places once your module is in CVS and
> working. Regarding the parser: I'm not making any recommendations, I asked
> because there have been suggestions at various times to reduce the number of
> different XML parsers used by Bioperl, we just didn't want to see your
> module using yet-another-one!
>
> It sounds like you don't have your own CVS account. Do you anticipate
> continuing to work on this and other modules or did you just want me to
> commit your code?
>
> 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 1:29 PM
> To: Brian Osborne
> Cc: bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] Bioperl support for AGAVE xml
>
> 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...
>
> 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
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
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