—
—
—
—
—
—
—
—

              
# BioPerl module for Bio::Tools::Pseudowise
#
# $Id: Pseudowise.pm,v 1.10.4.1 2006/10/02 23:10:32 sendu Exp $
# 
# Copyright Jason Stajich, Fugu Team 
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
HideShow 53 lines of Pod
=head1 NAME
Bio::Tools::Pseudowise - Results of one Pseudowise run
=head1 SYNOPSIS
  use Bio::Tools::Pseudowise;
  my $parser = Bio::Tools::Pseudowise->new(-file=>"pw.out");
  while(my $feat = $parser->next_result){
      push @feat, $feat;
  }
=head1 DESCRIPTION
Pseudowise is a pseudogene prediction program written by Ewan Birney
as part of the Wise Package. This module is the parser for the output
of the program.
http://www.sanger.ac.uk/software/wise2
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Jason Stajich
Previous committed by the Fugu Team 
Re-written by Jason Stajich jason-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object methods. 
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Pseudowise;
use strict;
use Symbol;
use Bio::Root::Root;
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::Gene::Exon;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Gene::Transcript;
use Bio::SeqFeature::Gene::GeneStructure;
use base qw(Bio::Tools::AnalysisResult);
sub _initialize_state {
    my ($self,@args) = @_;
    # first call the inherited method!
    $self->SUPER::_initialize_state(@args);
    # our private state variables
    $self->{'_preds_parsed'} = 0;
    $self->{'_has_cds'} = 0;
    # array of pre-parsed predictions
    $self->{'_preds'} = [];
    # seq stack
    $self->{'_seqstack'} = [];
}
HideShow 10 lines of Pod
=head2 analysis_method
 Usage     : $pseudowise->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
             /pseudowise/i.
 Returns   : String
 Argument  : n/a
=cut
#-------------
sub analysis_method { 
#-------------
    my ($self, $method) = @_;  
    if($method && ($method !~ /pseudowise/i)) {
        $self->throw("method $method not supported in " . ref($self));
    }
    return $self->SUPER::analysis_method($method);
}
HideShow 15 lines of Pod
=head2 next_feature
 Title   : next_feature
 Usage   : $seqfeature = $obj->next_feature();
 Function: Returns the next feature available in the analysis result, or
           undef if there are no more features.
 Example :
 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
           more features.
 Args    : none
See Also  L<Bio::SeqFeatureI>
=cut
sub next_feature {
    return shift->next_prediction(@_);
}
HideShow 17 lines of Pod
=head2 next_prediction
 Title   : next_prediction
 Usage   : while($gene = $pseudowise->next_prediction()) {
                  # do something
           }
 Function: Returns the gene of the Pseudowise result
           file. Call this method repeatedly until FALSE is returned.
 Example :
 Returns : a Bio::SeqFeature::Generic 
 Args    : none
See Also L<Bio::SeqFeature::Generic>
=cut
sub next_prediction {
    my ($self) = @_;
    # if the prediction section hasn't been parsed yet, we do this now
    $self->_parse_predictions unless $self->_predictions_parsed;
    # get next gene structure
    return $self->_prediction();
}
HideShow 11 lines of Pod
=head2 _parse_predictions
 Title   : _parse_predictions()
 Usage   : $obj->_parse_predictions()
 Function: Parses the prediction section. Automatically called by
           next_prediction() if not yet done.
 Example :
 Returns : 
=cut
sub _parse_predictions {
    my ($self) = @_;
    my $gene;
    my @genes;
    local $/= "\n";
    local($_);
    my %tags;
    while (defined( $_ = $self->_readline)){ 
        if( /^(Total codons|\S+)\s+:\s+(\S+)/ ) {
            $tags{$1} = $2;
        } elsif(m!^//! ) {
            if( $gene ) {
                $gene = undef;
                %tags = ();
            }
        } elsif (/Gene\s+(\d+)\s*$/i) {
            $gene = Bio::SeqFeature::Generic->new 
                ( -primary => 'pseudogene',
                  -source  => 'pseudowise',
                  -tag     => \%tags);
            push @genes, $gene;
        } elsif( /Gene\s+(\d+)\s+(\d+)/i ) {
            if( $1 < $2 ) {
                $gene->start($1);
                $gene->end($2);
                $gene->strand(1);
            } else {
                $gene->start($2);
                $gene->end($1);
                $gene->strand(-1);
            }
        } elsif (/Exon\s+(\d+)\s+(\d+)\s+phase\s+(\S+)/i) {
            my ($s,$e,$st) = ($1,$2,1);
            if( $s > $e) {
                ($s,$e,$st)=($e,$s,-1);
            }
            my $exon = Bio::SeqFeature::Generic->new 
                ( -start   => $s,
                  -end     => $e,
                  -strand  => $st,
                  -primary => 'exon',
                  -source  => 'pseudowise',
                  -tag     => {'frame'  => $3});
            $gene->add_sub_SeqFeature($exon);
        } 
    }
    $self->_add_prediction(\@genes);
    $self->_predictions_parsed(1);
}
HideShow 10 lines of Pod
=head1 _prediction
 Title   : _prediction()
 Usage   : $gene = $obj->_prediction()
 Function: internal
 Example :
 Returns : 
=cut
sub _prediction {
    my ($self) = @_;
    return shift(@{$self->{'_preds'} || []});
}
HideShow 10 lines of Pod
=head2 _add_prediction
 Title   : _add_prediction()
 Usage   : $obj->_add_prediction($gene)
 Function: internal
 Example :
 Returns : 
=cut
sub _add_prediction {
    my ($self, $gene) = @_;
    $self->{'_preds'} ||= [];
    if( ref($gene) =~ /ARRAY/ ) {
        push(@{$self->{'_preds'}}, @$gene);
    } else {
        push(@{$self->{'_preds'}}, $gene);
    }
}
HideShow 10 lines of Pod
=head2 _predictions_parsed
 Title   : _predictions_parsed
 Usage   : $obj->_predictions_parsed
 Function: internal
 Example :
 Returns : TRUE or FALSE
=cut
sub _predictions_parsed {
    my ($self, $val) = @_;
    $self->{'_preds_parsed'} = $val if $val;
    if(! exists($self->{'_preds_parsed'})) {
        $self->{'_preds_parsed'} = 0;
    }
    return $self->{'_preds_parsed'};
}
1;