[Bioperl-l] seq truncation by Bio::Tools::Run::Signalp

[Hilmar Lapp]

Marc, what you spotted is clearly a bug. Do you have cvs write access? 
If you don't yet, would you be comfortable with getting it and 
committing your changes yourself?

	-hilmar

On Wednesday, May 26, 2004, at 06:39  AM, Marc Logghe wrote:

> Hi,
> I don't know what your experience is with Bio::Tools::Run::Signalp, 
> but I was feeling a little uncomfortable about the current behaviour 
> of this package. The issue is that when you do:
> my @signals = $factory->run($seq)
> your sequence gets truncated to 50 aa !!!
> AFAIK, one expects of Bio::Tools::Run::* that your seq object remains 
> intact and that you only obtain your returned features, no ?
> Anyhow, this behaviour can be fixed with the patch below. Basically, 
> it passes the '-trunc 50' parameter to the signalp executable, which 
> has the same effect as first truncating your query seq to 50 aa.
> HTH,
> Marc
>
> *** /usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/Signalp.pm	Wed May 26 
> 15:21:55 2004
> --- Signalp.pm 	Wed May 26 13:20:23 2004
> *************** sub run {
> *** 179,184 ****
> --- 179,190 ----
>               $self->throw("cannot use filehandle");
>           }
>
> +   #first 50 aa is enough for signalp
> + 	if ($seq->length>50){
> +
> + 	    my $sub_seq = $seq->subseq(1, 50);
> + 	    $seq->seq($sub_seq);
> + 	}
>   	my $infile1 = $self->_writeSeqFile($seq);
>
>   	$self->_input($infile1);
> *************** sub run {
> *** 191,197 ****
> --- 197,207 ----
>   	my $in  = Bio::SeqIO->new(-file => $seq, '-format' =>'fasta');
>   	my $infile1;
>
> +   #first 50 aa is enough for signalp
>   	while ( my $tmpseq = $in->next_seq() ) {
> +
> + 	    my $sub_seq = $tmpseq->length > 50 ? $tmpseq->subseq(1,50) : 
> $tmpseq->seq;
> + 	    $tmpseq->seq($sub_seq);
>   	    $infile1 = $self->_writeSeqFile($tmpseq);
>   	}
>
> *************** sub _run {
> *** 233,239 ****
>        my ($self)= @_;
>
>        my ($tfh1,$outfile) = 
> $self->io->tempfile(-dir=>$self->tempdir());
> !      my $str =$self->executable." -t euk -trunc 50 
> ".$self->{'input'}." > ".$outfile;
>        my $status = system($str);
>        $self->throw( "Signalp call ($str) crashed: $? \n") unless 
> $status==0;
>
> --- 243,249 ----
>        my ($self)= @_;
>
>        my ($tfh1,$outfile) = 
> $self->io->tempfile(-dir=>$self->tempdir());
> !      my $str =$self->executable." -t euk ".$self->{'input'}." > 
> ".$outfile;
>        my $status = system($str);
>        $self->throw( "Signalp call ($str) crashed: $? \n") unless 
> $status==0;
>
> ***********************************************************
> Marc Logghe, Ph.D.
> Senior Scientist
> Scientific Computing Group
> Devgen nv
> Technologiepark 9
> As of March 1st, 2004 : Technologiepark 30
> B - 9052 Ghent-Zwijnaarde
> Belgium
> Tel: +32 9 324 24 88
> Fax: +32 9 324 24 25
>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------