[Bioperl-l] Bioperl support for AGAVE xml
brian_osborne at cognia.com
Mon Jul 19 13:54:37 EDT 2004
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?
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
> 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
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
> 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
> 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
> like to know what else is out there in terms of bioperl support.
> Many thanks for any comments/suggestions.
> Warmest Regards,
> Simon K. Chan
> Bioinformatics, Crosby Lab
> skchan at cs.usask.ca
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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