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

[Brian Osborne]

Dan,

If you do switch to SearchIO there's a section on creating BLAST reports as
HTML in Jason's HOWTO:

http://bioperl.org/HOWTOs/html/SearchIO.html


Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Dan Kortschak
Sent: Wednesday, February 12, 2003 9:04 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] StandAloneBlast returning Bio::SearchIO::blast was:
whereis Bio::Tools::Run::WrapperBase.pm?

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?

thanks
Dan

On Wed, 12 Feb 2003, Jason Stajich wrote:

> This is in a bug report on bugzilla.bioperl.org, can't remember the number
> off the top of my head but you can search for WrapperBase and I find it.
> It is a mis-packaging problem with 1.2.  You can get the file from
> http://bio.perl.org/SRC/branch-1.2, or from CVS, or wait for 1.2.1 when it
> comes out at the end of next week.
>
> -jason

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