[Bioperl-l] Re moteblast using Swissprot
manni122
markus.liebscher at gmx.de
Mon Apr 27 13:51:09 UTC 2009
Hi,
I want to retrieve the sequence identifier from the remoteblast interface
(Bio::Tools::Run::RemoteBlast). With this ID I want to look up annotations
stored in the Bio::DB::SwissProt.
I am using the example code from the RemoteBlast documentation. If I am
using a known sequence as input I get "Can't call method "next_hsp" on an
undefined value "?
This happens only with swissprot as database - the nr database works fine.
The accession code from nr is not accepted from the Bio::DB::SwissProt.
Is there something wrong with the database?
Here is the code I am using:
my $v = 1;
my @params = ('-prog' => 'blastp',
'-data' => 'nr',
'-expect' => '1e-10' ); #swissprot is not working
$Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'BLOSUM62';
my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
$v = 1;
my $r = $factory->submit_blast($proteinaa);
print STDERR "Need BLAST Analysis, waiting..." if( $v > 0 );
while ( my @rids = $factory->each_rid ) {
foreach my $rid ( @rids ) {
my $rc = $factory->retrieve_blast($rid);
if( !ref($rc) ) {
if( $rc < 0 ) {
$factory->remove_rid($rid);
}
print STDERR "." if ( $v > 0 );
sleep 5;
} else {
$factory->remove_rid($rid);
$result = $rc->next_result;
$hit = $result->next_hit;
$hsp = $hit->next_hsp;
$idneu = $hit->accession;
}
}
}
--
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