[Bioperl-l] Bio::SearchIO::psiblast

[Jason Stajich]

I think psiblast is deprecated all the functionality to parse PSIBLAST 
reports are in Bio::SearchIO::blast.

-jason
On Dec 6, 2004, at 1:32 PM, Liliana Davalos wrote:

> Hi,
>
> I am trying to parse the result of a psi-blast search using SearchIO. 
> I get thrown with the message at the bottom, although I am using the 
> textbook example:
>
> use Bio::SearchIO;
>
>     my $in = Bio::SearchIO->new( -format  => 'psiblast',
>                                  -file    => 'report.blastp' );
>
>     while ( my $blast = $in->next_result() ) {
>         foreach my $hit ( $blast->hits ) {
>             print "Hit: $hit\n";
>         }
>    }
>
> Error message:
>
> Can't locate object method "result_factory" via package 
> "Bio::SearchIO::psiblast" at 
> /usr/local/lib/perl5/site_perl/5.6.0/Bio/SearchIO/psiblast.pm line 
> 668, <GEN1> line 16.
>
> Does anyone have working examples?
>
> Thanks, Liliana
>
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>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/