[Bioperl-l] StandAloneBlast : 2 newbie questions

[Alexandre Irrthum]

Hello,

Two naive questions about the StandAloneBlast module. If it helps,
I am using Bioperl 0.7.0. with Perl 5.005_03.

Question 1.

In the following script, the call to blastall doesn't seem to work
because I modify the input record separator variable $/. The fields of
the BPlite object $blast_report are undef. No problem if let $/="\n". 
Is there a way to use StandAloneBlast while still changing $/ ?  

TEST SCRIPT :

#!/usr/bin/perl -w

use strict;
use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;

my @params = (program => 'blastx', database => 'SPEns');
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
$/ = "..";
open(SEQS, 'seqs') || die "Can't open : $!\n";
while(<SEQS>) {
  chomp;
  if (/([acgtn]{40,})/) {
    my $seq = Bio::Seq->new(-id => "test", -seq => $1);
    print "Sequence: ", $seq->seq(), "\n";
    my $blast_report = $factory->blastall($seq);
    print $blast_report->query, "\n";
  }
}
close(SEQS);

TEST INPUT FILE (seqs) :

..
catcagctaaacttgctggaggcaacccaatgaatgttccagcagccaagaagaggagggg
..
catcagcttcacttgctgtttgcaacccaatgagggttccagcagccaagtagaggagtgg
..
catcagcttcacttgctggagacaacccaatccgcagttccagcagccaagaagagggggg

Question 2.

I have to perform a large number a blast iterations and would like
to avoid accumulation of temporary input sequence files in /tmp.
Can I get the name of these files after each iteration to unlink them,
or is there another way ?


Thank you for your help.


Alexandre Irrthum