[Bioperl-l] Bioperl support for AGAVE xml
Simon K. Chan
skchan at cs.usask.ca
Mon Jul 19 15:17:59 EDT 2004
Ok, Jason. XML::SAX it is!
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.
Simon K. Chan
Bioinformatics, Crosby Lab
skchan at cs.usask.ca
Quoting Brian Osborne <brian_osborne at cognia.com>:
> 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
> > 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
> > 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
> one instead of the regexps?
> Yes, I'd like agave.pm added to CVS so I can commit changes/additions as
> 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
> > 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
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
More information about the Bioperl-l