[Bioperl-l] StandAloneBlast returning Bio::SearchIO::blast was: where is Bio::Tools::Run::WrapperBase.pm?

[Ewan Birney]

On Thu, 13 Feb 2003, Dan Kortschak wrote:

> Yup, that error is cleared up now. I still am having a problem getting a
> Bio::Tools::Blast object back from my StandAloneBlast. The returned object
> is a Bio::SearchIO::blast through the StandAloneBlast{_READMETHOD}
> variable is set to Blast. And since I want to do a $blast->to_html the
> script breaks there.
>
> Is there something that I'm missing here?

In Bioperl 1.2 we have moved from the (deprecated for a while now)
Bio::Tools::BLAST to the new, shiny, Bio::SearchIO (a Jason Staijch
production, staring all your favourite "classic" search algorithms, such
as BLAST, HMMER, Fasta - I believe Bio::SearchIO is in the running for
'Best Picture' as well as 'Best Event parsing framework')


anyway - I digress -


You want to be using the -writer format to the SearchIO factory, which in
StandAloneBlast, from reading the docs, looks ... hmmm... not sure


Peter S - any help here?


Dan - the new SearchIO writer functionality has everything the old
to_html has and more, so it is worth using it....