[Bioperl-l] Bioperl support for AGAVE xml

Brian Osborne brian_osborne at cognia.com
Mon Jul 19 12:57:46 EDT 2004


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. 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?

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 that
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

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