[Bioperl-l] BLASTing with a seqio/seq object...
st537 at york.ac.uk
Tue Nov 28 06:02:07 EST 2006
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
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...
$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;
$remote_blast = Bio::Tools::Run::RemoteBlast->new (
-prog => 'blastp', -db => 'nr', -expect => '1e-15' );
$blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq);
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