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# $Id: Signalp.pm,v 1.8.4.2 2006/10/19 18:44:40 jason Exp $
# Parser module for Signalp Bio::Tools::Signalp
#
# 
# Based on the EnsEMBL module
# Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally
# written by Marc Sohrmann (ms2@sanger.ac.uk) Written in BioPipe by
# Balamurugan Kumarasamy <savikalpa@fugu-sg.org> Cared for by the Fugu
# Informatics team (fuguteam@fugu-sg.org)
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
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=head1 NAME
Bio::Tools::Signalp - parser for Signalp output
=head1 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;
   }
 }
=head1 DESCRIPTION
C<SignalP> predicts the presence and location of signal peptide
cleavage sites in amino acid sequences.
L<Bio::Tools::Signalp> parses the output of C<SignalP> to provide a 
L<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 C<score()> attribute contains the
NN probability of this being a true signal peptide.
=head1 FEEDBACK
=head2 Mailing Lists
 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
=head2 Reporting Bugs
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:
  http://bugzilla.open-bio.org/
=head1 AUTHOR
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)
=head1 CONTRIBUTORS
Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Tools::Signalp;
use strict;
use Bio::SeqFeature::Generic;
use base qw(Bio::Root::Root Bio::Root::IO);
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=head2 new
 Title   : new
 Usage   : my $obj = new Bio::Tools::Signalp();
 Function: Builds a new Bio::Tools::Signalp object
 Returns : Bio::Tools::Signalp
 Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO
=cut
sub new {
      my($class,@args) = @_;
      my $self = $class->SUPER::new(@args);
      $self->_initialize_io(@args);
      return $self;
}
HideShow 10 lines of Pod
=head2 next_result
 Title   : next_result
 Usage   : my $feat = $signalp->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::Generic
 Args    : none
=cut
sub next_result {
        my ($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();
                  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");
                  }
                   
              }
           }
         
        }
}
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=head2 _parse_hmm_result
 Title   : _parse_hmm_result
 Usage   : $self->_parse_hmm_result(\%feature)
 Function: Internal (not to be used directly)
 Returns : hash of feature values
 Args    : hash of more feature values
=cut
sub _parse_hmm_result {
    my ($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;
        }
    }
}
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=head2 _create_feature
 Title   : _create_feature
 Usage   : $self->create_feature(\%feature)
 Function: Internal (not to be used directly)
 Returns : hash of feature values
 Args    : hash of more feature values
=cut
sub _create_feature {
    my ($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; 
}
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=head2 _seqname
 Title   : _seqname
 Usage   : $self->_seqname($name)
 Function: Internal (not to be used directly)
 Returns :
 Args    :
=cut
sub _seqname{
    my ($self,$seqname)=@_;
    if (defined$seqname){
        $self->{'seqname'}=$seqname;
    }
    return $self->{'seqname'};
}
HideShow 10 lines of Pod
=head2 _fact1
 Title   : _fact1
 Usage   : $self->fact1($fact1)
 Function: Internal (not to be used directly)
 Returns : 
 Args    :
=cut
sub _fact1{
    my ($self, $fact1)=@_;
    if (defined $fact1){
       $self->{'fact1'}=$fact1;
    }
    return $self->{'fact1'};
}
1;