[Bioperl-l] Re: HitTableWriter.pm and HSPTableWriter.pm

[Jason Stajich]

These aren't compatable in 1.0 - working to phase out psiblast.

your reported bug should be fixed by Steve's latest changes.



On Sun, 3 Nov 2002, Linda Sperling wrote:

> OK, I am an idiot. All I needed to do was specify the correct
> Bio::SearchIO module i.e. psiblast and not blast.
>
> However, there IS a bug!
>
> If I try to use default column values (at least on blastx output) then the
> parser only writes zeroes. I need to specify columns. Maybe this is not a
> problem with bona fide psiblast reports?
>
> This gives zeroes:
> my $writer = Bio::SearchIO::Writer::HSPTableWriter->new();
>
> This works:
> my $writer = Bio::SearchIO::Writer::HSPTableWriter->new( -columns =>
> \@columns );
>
> (with an appropriate selection of some columns).
>
> Sorry to bother you guys - I should have exhausted all possibilites
> before writing.
> Please keep up the great work.
> Linda Sperling
>
>

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