Bio::Tools
Signalp
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Summary
Bio::Tools::Signalp - parser for Signalp output
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Tools::Signalp;
my $parser = Bio::Tools::Signalp->new(-fh =>$filehandle );
while( my $sp_feat = $parser->next_result ) {
if ($sp_feat->score > 0.9) {
push @likely_sigpep, $sp_feat;
}
}
Description
SignalP predicts the presence and location of signal peptide
cleavage sites in amino acid sequences.
Bio::Tools::Signalp parses the output of SignalP to provide a
Bio::SeqFeature::Generic object describing the signal peptide
found, if any. It returns a variety of tags extracted from the NN and HMM
analysis. Most importantly, the score() attribute contains the
NN probability of this being a true signal peptide.
Methods
Methods description
Title : new
Usage : my $obj = Bio::Tools::Signalp->new();
Function: Builds a new Bio::Tools::Signalp object
Returns : Bio::Tools::Signalp
Args : -fh/-file => $val, # for initing input, see Bio::Root::IO |
Title : next_result
Usage : my $feat = $signalp->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none |
Title : _parse_hmm_result
Usage : $self->_parse_hmm_result(\%feature)
Function: Internal (not to be used directly)
Returns : hash of feature values
Args : hash of more feature values |
Title : _create_feature
Usage : $self->create_feature(\%feature)
Function: Internal (not to be used directly)
Returns : hash of feature values
Args : hash of more feature values |
Title : _seqname
Usage : $self->_seqname($name)
Function: Internal (not to be used directly)
Returns :
Args : |
Title : _fact1
Usage : $self->fact1($fact1)
Function: Internal (not to be used directly)
Returns :
Args : |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;} | sub next_result
{ my ($self) = @_;
while (my $line=$self->_readline()) {
chomp $line;
if ($line=~/^\>(\S+)/) {
$self->_seqname($1);
}
elsif ($line=~/max\.\s+Y\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
$self->_fact1($2);
}
elsif ($line=~/mean\s+S\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
my $fact2 = $2;
if ($fact2 eq 'YES' and $self->_fact1 eq 'YES') {
my $line = $self->_readline();
chomp $line;
if ($line =~ /\s+D\s+.*/) {
$line = $self->_readline();
}
my $end;
if ($line =~ /Most likely cleavage site between pos\.\s+(\d+)/) {
my $end = $1;
my (%feature);
$feature{seq_id} = $self->_seqname;
$feature{start} = 1;
$feature{end} = $end;
$feature{source_tag} = 'Signalp';
$feature{primary}= 'signal_peptide';
$self->_parse_hmm_result(\%feature);
my $new_feat = $self->_create_feature (\%feature);
return $new_feat;
}
else {
$self->throw ("parsing problem in signalp");
}
}
}
}} | sub _parse_hmm_result
{ my ($self, $feature_hash) = @_;
while(my $line = $self->_readline){
chomp $line;
if($line =~ /Prediction: (.+)$/){
$feature_hash->{hmmProdiction} = $1;
}elsif($line =~ /Signal peptide probability: ([0-9\.]+)/){
$feature_hash->{peptideProb} = $1;
}elsif($line =~ /Signal anchor probability: ([0-9\.]+)/){
$feature_hash->{anchorProb} = $1;
last;
}
}} | sub _create_feature
{ my ($self, $feat) = @_;
my $feature = Bio::SeqFeature::Generic->new(
-seq_id => $feat->{name},
-start => $feat->{start},
-end => $feat->{end},
-score => $feat->{score},
-source => $feat->{source},
-primary => $feat->{primary},
-logic_name => $feat->{logic_name},
);
$feature->score($feat->{peptideProb});
$feature->add_tag_value('peptideProb', $feat->{peptideProb});
$feature->add_tag_value('anchorProb', $feat->{anchorProb});
$feature->add_tag_value('evalue',$feat->{anchorProb});
$feature->add_tag_value('percent_id','NULL');
$feature->add_tag_value("hid",$feat->{primary});
$feature->add_tag_value('SignalpPrediction', $feat->{hmmProdiction});
return $feature;} | sub _seqname
{ my ($self,$seqname)=@_;
if (defined$seqname){
$self->{'seqname'}=$seqname;
}
return $self->{'seqname'};} | sub _fact1
{ my ($self, $fact1)=@_;
if (defined $fact1){
$self->{'fact1'}=$fact1;
}
return $self->{'fact1'};
}
1;} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted va the
web:
https://redmine.open-bio.org/projects/bioperl/
# Please direct questions and support issues to bioperl-l@bioperl.org
Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp
originally written by Marc Sohrmann (ms2_AT_sanger.ac.uk). Written in BioPipe by
Balamurugan Kumarasamy savikalpa_AT_fugu-sg.org. Cared for by the Fugu
Informatics team (fuguteam_AT_fugu-sg.org)
Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _