[Bioperl-l] pointer to pseudowise ?

George Hartzell hartzell at kestrel.alerce.com
Thu Sep 29 17:28:18 EDT 2005

Ewan Birney writes:
 > George Hartzell wrote:
 > > bioperl-run has support for pseudowise, but I can't find it.  It
 > > doesn't seem to be in the wise2.20, 2.1.23c, or 2.1.16b distributions.
 > > 
 > > Anyone know what's up?
 > > 
 > :) it is in the 2.2.3-rc7 release which has not made the light of day
 > for the last 1.5 years. you know who you can blame :)
 > [...]

I picked up the 2.2.3-rc7 release and it passes it's tests.

bioperl-run's t/Pseudowise.t isn't working out so well.

It looks like it's expecting pseudowise to find a single gene with two
exons from 163 to 626, but running pseudowise by hand based on the
BIOPERLDEBUG output just generates a single-exon gene from 865-900
(which is properly represented in the bioperl objects).

Does it work for other folk?

Any suggests for straightening this out?


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