Bioperl?

Philipp Pagel pagel at abraxas.magic.lan
Tue Apr 18 20:59:18 EST 2000


		Hi!

Are there any bioperl users here?

I am trying to write a littel script to perform remote blast searches witha
bunch of sequences, but can't get the Blast module to work.

         %runParam = (
                      -seqs     => [$seq],
                      -method   => 'remote',
                      -prog     => 'blastn',
                      -database => 'nr',
                      -version  => 2,      # BLAST2
                      -html     => 'on',
                      -descr    => 250,
                      -align    => 250,
                      -expect   => 10,
                      -gap      => 'on',
                      -matrix   => 'PAM250',
                      -email    => undef,  # don't send report via e-mail
                      -filter   => undef,  # use default
                      -gap_c    => undef,  # use default
                      -gap_e    => undef,  # use default
                      -word     => undef,  # use default
                      -min_len  => undef,  # use default
        );


        # run the DB inquiry

        $blastObj = Bio::Tools::Blast->new(
                -run => \%runParam,
                -parse   => 1,
                -signif  => '1e-10',
                -strict  => 1,
        );

but all I get is a couple of supposedley harmless warning and finally:

Can't locate object method "layout" via package "Bio::Seq" at
/usr/lib/perl5/site_perl/5.005/Bio/Tools/Blast/Run/Webblast.pm line 804,
<GEN0> chunk 36.

What is the point I am missing?

cu
	Philipp

-- 
Dr. Philipp Pagel
Cellular and Molecular Physiology         phone: (203) 785-6835	
SHM BE-30
Yale University
333 Cedar ST
New Haven, CT 06520





More information about the Bio-soft mailing list