Bioperl: running local blasts

[Joey Morris]

Yes, and in Bio/Root/Object.pm it has

@EXPORT_OK = qw($VERSION &find_object &stack_trace &containment &_rearrange);  

which I assume gives other modules permission to use its _rearrange.

Joey


Alan Williams wrote on Jun 22 at 01:24 pm:
> 
> Does your LocalBlast.pm module have the following near the top:
> 
>    use Bio::Root::Object    qw(&_rearrange);
> 
> -A
> 
> ---------------------------------
> Alan Williams
> Neomorphic, Inc.
> Alan@Neomorphic.com
> 510-981-8513
> ---------------------------------
> 
> On Wed, 21 Jun 2000, Joey Morris wrote:
> 
> > Date: Wed, 21 Jun 2000 15:58:13 -0400
> > From: Joey Morris <rjmorris@unity.ncsu.edu>
> > To: vsns-bcd-perl@lists.uni-bielefeld.de
> > Subject: Bioperl: running local blasts
> > 
> > Can anyone tell me if they are successfully running local blast searches
> > using the LocalBlast.pm module? I just downloaded 0.6.1 and I get this error
> > when running a local blast:
> > 
> > *** 1 Blast reports produced fatal errors:
> > Undefined subroutine &Bio::Root::Object::_rearrange called at
> > /local/lib/perl/lib/Bio/Tools/Blast/Run/LocalBlast.pm line 309.
> > 
> > I experienced the same issue with 0.6.0 but not with the 0.05.1 release.
> > I've reported it as a bug but there's been no progess on it apparently.
> > 
> > Thanks,
> > Joey
> > 
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