[Bioperl-l] estwisedb

[Ewan Birney]

On Thu, 29 Aug 2002, Mick Watson wrote:

> Hi
> 
> Does anyone know of any modules for parsing the output from estwisedb 
> (part of the Wise2 package)??

I don't (and ... I wrote estwisedb!) but it should not be that hard to
parse, unless you want the alignments at which point it is likely to
become fearsomely hard as 

  (a) the alignment dumping is somewhat arcane

  (b) there is no bioperl alignment model which sensibly handles
frameshifts



what do you want to do with the results?


The "right thing" to do would be to write a SearchIO system for this, and
I will look into this now to educate myself for how to write SearchIO
parsers...






> 
> Thanks
> Mick
> 
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