[Bioperl-l] Re: HitTableWriter.pm and HSPTableWriter.pm
Sun, 3 Nov 2002 17:52:19 -0500 (EST)
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 at cgt.mc.duke.edu