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

[Linda Sperling]

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

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