[Bioperl-l] question about SeqIO and BSML DTD

[Jason Stajich]

Short answer is no - there is no easy way to do it because of the way
this module is written.  I have no idea how different 3.1 is from 2.2 as
to how much of a code change this is.


This module is still looking for an 'owner' or someone to maintain it -
preferrably someone who actually uses BSML so they can be closer to some
of the nuances of the format.  Volunteers welcome.

-jason

On Mon, 11 Aug 2003, Susan Cassidy wrote:

> Hi,
> It looks like the current (1.2.2) bioperl bsml functions are set up to use
> the BSML 2.2 DTD.  I would like to use the 3.1 DTD instead.  Is there some
> easy way to have things like SeqIO create BSML output using the 3.1 DTD?
> I'm not sure how the internal handling of all the DTD stuff works, but I
> do see that the DTD URL is hard-coded in bsml.pm to be
> "http://www.labbook.com/dtd/bsml2_2.dtd".
>
> It would be wonderful if it were as easy as changing that!  But, I won't
> hold my breath!
>
> I'm doing some experimentation with converting sequences from formats such
> as Genbank into BSML, and this makes it really simple.
>
> Please reply to this email address and not just to the list, as I don't
> subscribe to it.
>
> Any advice appreciated.
>
> Thanks,
> Susan Cassidy

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu