[Bioperl-l] repost the problem --- Re: bl2seq hang and its performace

[Liu Haifeng]

Anyone can help?  Really urgent!

Haifeng Liu
----- Original Message ----- 
From: "Liu Haifeng" <lhaifeng at dso.org.sg>
To: <bioperl-l at portal.open-bio.org>
Sent: 2003年12月12日 14:49
Subject: bl2seq hang and its performace


> Hi all,
>
> I noticed that one of my program written using bioperl-1.2.3 runs very
slow
> and consumes huge memory, and I doubted that it is due to the call of
bl2seq
> in the program.  Thus, I wrote a small program (bl2seq sequences against
> themselves from a fasta file) below to see if it is the ture:
>
>
> #!/usr/bin/perl -w
>        use Bio::SeqIO;
>       use Bio::Tools::Blast;
>        use Bio::Tools::Run::StandAloneBlast;
>        use Bio::Tools::BPlite;
>
>        my $infile =shift;
>        my $sno=0;
>        my $blastalgo="blastp"; #blastp ,blastx, tblastn, tblastx
>        my $pin = Bio::SeqIO->new('-file' => "$infile", '-format' =>
> 'Fasta');
>       while ( my $proseq = $pin -> next_seq()) {
>           $sno++;
>           print "bl2seq $sno ..............................\n";
>           my @params=('program' => $blastalo);
>           my $factory= Bio::Tools::Run::StandAloneBlast->new(@params);
>           $factory->io->_io_cleanup();
>           my $report=$factory->bl2seq($proseq, $proseq);
>           while (my $hsp=$report->next_feature) {
>               #only need the first hsp
>               $report->close();
>            }
>           undef $report;
>      }
>       print "running is over\n";
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> The program runs ok for the small fastat file.  However, when I input a
> fasat file around 2.6M containing 10,000 protein sequences, the program
> hangs when it compare the 1782th sequence.  Also I noticed that the
program
> has consume 12M of memory at that time.   I searched the archive that
there
> have been similar bl2seq problem occurred.  However, it should have been
> solved in the latest version.
>
> Anyone can show me some clues to improve the performance of calling
bl2seq?
> Thank you.
>
> Regards
> Haifeng Liu
>
>
>