[Bioperl-l] starting out with Boulder

[Lincoln Stein]

I hate to differ, Jason, but if you look at bioperl.pod and search for BLAST, 
the very first thing it does is to tell you to use Bio::Tools::Blast. 
(Actually first it tells you to use Bio::Tools::BPLite, and then it tells you 
to use Bio::Tools::Blast.) 

You have to go several more pages into the documentation before you get a 
mention of Bio::SearchIO.

Now, I know that the mailing list word is to use Bio::SearchIO for this, but 
until the official .pod documentation is changed, it is vital that we speak 
with one voice!

Lincoln

=head1 Examples/ Directory

There are many scripts included in the distribution.
Here are brief descriptions of the scripts in the I<examples/> directory:
...

I<examples/BioPerlBlast.pl> - script that takes multiple query sequences
and queries a database with Blast

I<examples/blast/*pl> - a set of scripts showing how to use Blast.pm.
Please see L<Bio::Tools::Blast> for more information



On Tuesday 20 August 2002 04:03 pm, Jason Stajich wrote:
> NO!
>
> Use
>
> Bio::SearchIO
>
> On Tue, 20 Aug 2002, Lincoln Stein wrote:
> > Boulder is entirely deprecated.  Use the BioPerl Bio::ToolsBlast module.
> >
> > Lincoln
> >
> > On Tuesday 20 August 2002 03:27 pm, skw p wrote:
> > > hello list,
> > > i have a set of tblastx results i need to parse out. I
> > > want to use Boulder
> > > for the job,after making modifications if any needed.
> > > I have no clue how to get
> > > started with this package, though!
> > > the documentation doesnt help me much- is there any
> > > other online manual
> > > help etc?
> > > thanks alot
> > > skw
> > >
> > >
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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