[Bioperl-l] Enquery about the Bio::Tools::Run::Alignment::Blat module

pan tong nickytong at gmail.com
Thu Oct 16 17:28:26 EDT 2008


Dear bioperl team,

I'm a graduate student. I've just begun using bioperl to conduct my
research. I found the modules provided by bioperl very useful. Besides,
there are many documents describing each module which is very helpful.

However, when I search the Blat module, there seems to be little example or
document about it. I have problems while using the blat module.

Here is my code:
----------------------------------------------------------------------------------------------------------------
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
use Bio::Tools::Alignment::Blat;

my $in= Bio::SeqIO->new(-file=>'124_Dmel_Enc[1][1].fa.txt' , '-format' =>
'Fasta' );
while ( my $seq_object = $in->next_seq() )
{
    my $seq=$seq_object->seq();
    #print "$seq\n";
    my $factory = Bio::Tools::Alignment::Blat->new();
    my $DB='D.melanogaster';
    my @feats = $factory->run($seq_object,$DB);
}
---------------------------------------------------------------------------------------------------------------
When I excute it, the program exit with "Can't locate object method "new"
via package "Bio::Tools::Alignment::Blat"..."
Can you help modify my code? Or can you give me a detailed sample code of
Blat so that I can refer?
By the way, I need to specify Genome with D.melanogaster when I call the
blat module.

Thank you very much and look forward to your reply.

Yours,

Pan

--
Department of Quantitative Science
M.D. Anderson Cancer Center
Houston, Tx, 77054


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