Hi,

I am trying to run a remote blast on a fasta file that is provided to me. Here is my code:


use Bio::SeqIO;
use Bio::Tools::Run::RemoteBlast;
my $Seq_in = Bio::SeqIO->new (-file => 'protein.fa',-format => 'fasta');
my $query = $Seq_in->next_seq();
my $factory = Bio::Tools::Run::RemoteBlast->new(
'-prog' => 'blastp',
'-data' => 'swissprot',
_READMETHOD => "Blast"
);
my $blast_report = $factory->submit_blast($query);
my $max_number = 100;
my $trial = 0;
while ( my @rids = $factory->each_rid ) {
print STDERR "\nSorry, maximum number of retries $max_number exceeded\n" ;
$trial++;
print STDERR "waiting... ".(5*$trial)." units of time\n" ;
# RID = Remote Blast ID (e.g: 1017772174-16400-6638)
foreach my $rid ( @rids ) {
my $rc = $factory->retrieve_blast($rid);
if( !ref($rc) ) {
if( $rc < 0 ) {
# retrieve_blast returns -1 on error
$factory->outfile('blast.out');
}
# retrieve_blast returns 0 on ’job not finished’
sleep 5*$trial;
}else {
#---- Blast done ----
$factory->outfile('blast.out');
my $blast_report = $factory->blastall($query);
my $result = $blast_report->next_result;
while( my $hit = $result->next_hit ()){
print "\thit name is: ", $hit->name(),
" significance: ", $hit->significance(), "\n";}
}
}
}


However I get and error that says,

Can't locate object method "outfile" via package Bio::Tools::Run::RemoteBlast at line 30;


I want a outfile in txt format. I tried changing blast.txt but doesn't work. Any suggestions of how to run this remote blast and get the file in text format?