[Bioperl-l] How put tmp file in the tmp directory when using Bio::Tools::Run::StandAloneBlastPlus?

Peng Yu pengyu.ut at gmail.com
Sun Jun 6 18:52:18 EDT 2010

The following perl program generate tmp files at the current
directory, which is annoying. Is there a way to put the tmp files in a
tmp directory say /tmp?

#!/usr/bin/env perl

use strict;
use warnings;
use Bio::Tools::Run::StandAloneBlastPlus;
use Bio::Perl;

my $factory = Bio::Tools::Run::StandAloneBlastPlus->new();

my $seq1 = Bio::Perl::read_sequence('first.fa');
my $seq2 = Bio::Perl::read_sequence('second.fa');
print $seq1->seq, "\n";
print $seq2->seq, "\n";

my $blast_result=$factory->bl2seq(-method=>'blastn',
  -query=> $seq1,
  -subject=> $seq2


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