[Bioperl-l] BLASTing with a seqio/seq object...

Samantha Thompson st537 at york.ac.uk
Tue Nov 28 06:02:07 EST 2006


Hi,
I am trying to learn bioperl and I'm attempting a few basic thing! I 
seem to be ok with reading in and outputting sequences and files now I 
am trying to do a simple BLAST search using a sequence (a sequence 
object in fact). The code I am attempting to run is at the bottom of the 
message...
I am probably making a dumb mistake and don't understand the 
capabilities of the objects well enough, but the info for the 
remoteblast->submit_blast function says that it can take sequences as an 
argument, I've also tried sending the fasta file name containing my 
sequence as an argument to submit_blast,  with the same result.... I 
have also tried sending $seqio_obj->next_seq...........  i.e the 
following error message displayed on my terminal:

Can't call method "submit_blast" on an undefined value at bioptest2.pl 
line 22, <GEN0> line 1.

I haven't got around to figuring out how to process the returned data 
from this yet, just trying to get the function to run first!
Thanks for any help that anyone can offer me with this...

Samantha Thompson

#********************************


use Bio::Seq;
use Bio::SeqIO;

use Bio::Tools::Run::RemoteBlast;
use Bio::SearchIO;

#seq bit

$seq_obj = Bio::Seq->new(-format => 'fasta');

$seqio_obj = Bio::SeqIO->new(-file => 
"/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta');

$seq_obj = $seqio_obj->next_seq;



#blast bit

$remote_blast = Bio::Tools::Run::RemoteBlast->new (
         -prog => 'blastp', -db => 'nr', -expect => '1e-15' );

$blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq);




#end


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