Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Signalp
<![CDATA[
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::Runnable::Protein::Signalp
=head1 SYNOPSIS
my $signalp = Bio::EnsEMBL::Analysis::Runnable::Protein::Signalp->new(
-query => $seq,
-analysis => $ana,
);
$signalp->run;
my @results = @{$signalp->output};
=head1 DESCRIPTION
=cut
package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Signalp;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation;
use Bio::SeqIO;
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation);
sub multiprotein{
my ($self) = @_;
return 0;
}
#
# we over-ride write_seq_file because Signalp works best
# if only the first 50 a.a. of the protein is supplied
sub write_seq_file{
my ($self, $seq, $filename) = @_;
if(!$seq){
$seq = $self->query;
}
if(!$filename){
$filename = $self->queryfile;
}
my $seqout = Bio::SeqIO->new(
-file => ">".$filename,
-format => 'Fasta',
);
eval{
my $init_seq = substr($seq->seq, 0, 50);
my $newseqobj = Bio::Seq->new(-id => $seq->display_id,
-seq => $init_seq);
$seqout->write_seq($newseqobj);
};
if($@){
throw("FAILED to write $seq to $filename Runnable:write_seq_file");
}
return $filename;
}
sub run_analysis {
my ($self) = @_;
throw("Error running ".$self->program." on ".$self->queryfile)
unless ((system($self->program . " -t euk "
.$self->queryfile
. " > ".$self->resultsfile)) == 0);
}
sub parse_results {
my ($self) = @_;
my ($fh);
my $resfile = $self->resultsfile;
if (-e $resfile) {
# it's a filename
if (-z $resfile) {
# no hits
return;
}else {
open ($fh, "<$resfile") or throw ("Error opening $resfile");
}
}else {
# it'a a filehandle
$fh = $resfile;
}
# parse
my (@fps, $id, $fact1, $fact2, $end);
while (<$fh>) {
chomp;
if (/^\>(\S+)/) {
$id = $1;
}
elsif (/max\.\s+Y\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
$fact1 = $2;
}
elsif (/mean\s+S\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
$fact2 = $2;
if ($fact1 eq "YES" && $fact2 eq "YES") {
my $line = <$fh>;
if ($line =~ /Most likely cleavage site between pos\.\s+(\d+)/) {
$end = $1;
}
else {
$self->throw ("parsing problem in ".$self->program);
}
my $fp = $self->create_protein_feature(1, $end, 0, $id, 0, 0,
'Sigp', $self->analysis,
0, 0);
push @fps, $fp;
}
}
}
close($fh);
$self->output(\@fps);
}
1;
]]>