Good day perl people.I have been working on some light perl projects. I have a project were i need to use the module Blast plus and i require some help.

I have this code

It is a very simple Blast Plus script which works as far as the blasting is concerned. My problem is that it also creates a lot of blast reports.

$seq = "MGPTSGPSLLLLLLTHLPLALGSP";

my ($hit, $frac, $eval) = blast($seq);

print "$hit\t$frac\t$eval\n";

sub blast {
    use strict;
    use Bio::Tools::Run::StandAloneBlastPlus;
    use Bio::Seq;
    use Bio::SearchIO;
    
    my $seq = $_[0];
    my $seq_obj = Bio::Seq->new(-id  =>"test", -seq =>$seq);
    my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
        -db_name => 'db',
    );
    
    my $report = $fac->blastp( -method => 'blastp',
        -query => $seq_obj,
    );
    
    my $hit = $report->next_hit();
    my $hit_name = $hit->name();
    $hit_name =~ s/\w{3}//;
    $hit_name;
    my $hsp = $hit->next_hsp();
    my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
    $frac_cons = $frac_cons*100;
    my $evalue = $hsp->evalue();
    return ($hit_name, int($frac_cons), $evalue);
}

[download]

The files which are created are "somename.fas" which gives the sequence which is being blasted and a BLASTP report "somename.file". So here comes the question: Is it possible to tell Blast Plus that i don't want anyfiles created?

I will be doing allot of blasting and i don't want to end up with gazillion(estimation) files on the server. If you see some errors or mistakes i would also of course appreciate help.

I have mostly been using http://www.bioperl.org/wiki/HOWTO:BlastPlus. But i did not see anything there which helped me.

Thank you in advance.

In reply to Blast Plus help. by Robbih

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