[Bioperl-l] HMMER/Results

[Ewan Birney]

On Thu, 4 Jul 2002, Mick Watson wrote:

> Version 0.7.2, the bioperl thats shipped with Ensembl :o)

Dead branch... Sorry Mick - you will need to do some funkiness in your
local install.

Ensembl will eventually move to the 1.0 trunk of bioperl, but will take
teh summer to get there.




>
> Jason Stajich wrote:
>
> > I believe this is already fixed as of bioperl-1.0.1
> > Can you report what version of bioperl or the revision ID for that
> > module (% perldoc -m Bio::Tools::HMMER::Result | grep Id)
> >
> > -j
> >
> > On Thu, 4 Jul 2002, Mick Watson wrote:
> >
> > > Hi
> > >
> > > In Bio::Tools::HMMER::Results, line 348 has the code:
> > >
> > >     $new = Bio::Tools::HMMER::Results->new();
> > >
> > > This is in the &filter_on_cutoff method.
> > >
> > > However, &new in the same module complains if you don't give it a -type
> > > argument!
> > >
> > > The correct line should be:
> > >
> > >     $new = Bio::Tools::HMMER::Results->new(-type => 'hmmsearch');
> > >
> > > There should also be a "return $new;" as the last line in the method
> > >
> > > Thanks
> > > Mick
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
>
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