[Bioperl-l] starting out with Boulder

[Ewan Birney]

On Tue, 20 Aug 2002, Lincoln Stein wrote:

> I apologize for the pissy letter.  The truth is that I was fooled by the 
> bioperl.pod file myself.  Rather than complain, I have removed all references 
> to Bio::Tools::Blast and BPLite from bioperl.pod.  I would like to go ahead 
> and move the relevant example scripts to the CVS attic.  Any objections?

None at all!


> 
> Lincoln
> 
> On Tuesday 20 August 2002 04:21 pm, Jason Stajich wrote:
> > This is very old documentation, I guess I will try and carve out time for
> > updating this at some point.
> >
> > On Tue, 20 Aug 2002, Lincoln Stein wrote:
> > > 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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> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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