Bio::Tools Signalp
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Summary
Bio::Tools::Signalp - parser for Signalp output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::Generic
Inherit
Bio::Root::IO Bio::Root::Root
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
newDescriptionCode
next_resultDescriptionCode
_parse_hmm_resultDescriptionCode
_create_featureDescriptionCode
_seqnameDescriptionCode
_fact1DescriptionCode
Methods description
newcode    nextTop
 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
next_resultcodeprevnextTop
 Title   : next_result
Usage : my $feat = $signalp->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none
_parse_hmm_resultcodeprevnextTop
 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
_create_featurecodeprevnextTop
 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
_seqnamecodeprevnextTop
 Title   : _seqname
Usage : $self->_seqname($name)
Function: Internal (not to be used directly)
Returns :
Args :
_fact1codeprevnextTop
 Title   : _fact1
Usage : $self->fact1($fact1)
Function: Internal (not to be used directly)
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
      my($class,@args) = @_;

      my $self = $class->SUPER::new(@args);
      $self->_initialize_io(@args);

      return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
        my ($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();
                  
                  ###########################################
# modification to suit new SignalP output
###########################################
chomp $line; #print STDERR "********** <$line>\n";
if ($line =~ /\s+D\s+.*/) { $line = $self->_readline(); } #print STDERR "********** <$line>\n";
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 { $self->throw ("parsing problem in signalp"); } } } }
}
_parse_hmm_resultdescriptionprevnextTop
sub _parse_hmm_result {
    my ($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} = $1;
            last;
        }
    }
}
_create_featuredescriptionprevnextTop
sub _create_feature {
    my ($self, $feat) = @_;

    # create feature object
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 $feature;
}
_seqnamedescriptionprevnextTop
sub _seqname {
    my ($self,$seqname)=@_;

    if (defined$seqname){
        $self->{'seqname'}=$seqname;
    }
    return $self->{'seqname'};
}
_fact1descriptionprevnextTop
sub _fact1 {
    my ($self, $fact1)=@_;

    if (defined $fact1){
       $self->{'fact1'}=$fact1;
    }
    return $self->{'fact1'};
}



1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
 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
Support Top
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.
Reporting BugsTop
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/
AUTHORTop
# 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)
CONTRIBUTORSTop
Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _