[Bioperl-l] blat format parser for Bio::SearchIO?

[Jason Stajich]

Bala wrote Bio::Tools::Blat to handle the psl format.
But it would be good to have a psl parser in SearchIO.  Also handling pslx
would be good as you could build the whole alignment string information
too into HSPs.

I did made sure the blast parser works for jim's pseudo-blast-like output
-out=wublast or -out=blast

Would be good to have psl, pslx, and axt parsers in SearchIO though and
would be great if you wanted to work on it!

-jason

On Fri, 18 Apr 2003, Matthew Betts wrote:

> Hi,
>
> Is anyone working on a parser of blat's output format for Bio::SearchIO?
> I'm wondering whether to try writing my own...
>
> Thanks,
>
> Matthew
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu