Raw content of Bio::Tools::Pseudowise
<![CDATA[# BioPerl module for Bio::Tools::Pseudowise
#
# Copyright Fugu Team
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=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, $feat;
}
=head1 DESCRIPTION
Pseudowise is a pseudogene prediction program written by Ewan Birney as part of the
Wise Package. This module is the parser for the output of the program.
http://www.sanger.ac.uk/localsw/wise2
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Fugu Team
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Pseudowise;
use vars qw(@ISA);
use strict;
use Symbol;
use Bio::Root::Root;
use Bio::Tools::AnalysisResult;
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::Gene::Exon;
use Bio::Tools::Run::WrapperBase;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Gene::Transcript;
use Bio::SeqFeature::Gene::GeneStructure;
@ISA = qw(Bio::Tools::AnalysisResult);
sub _initialize_state {
my ($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'} = [];
}
=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);
}
=head2 next_prediction
Title : next_prediction
Usage : while($gene = $pseudowise->next_prediction()) {
# do something
}
Function: Returns the gene of the Pseudowise result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : a Bio::SeqFeature::Generic
Args :
=cut
sub next_prediction {
my ($self,$filehandle) = @_;
my $gene;
# if the prediction section hasn't been parsed yet, we do this now
$self->_parse_predictions($filehandle) unless $self->_predictions_parsed();
# get next gene structure
$gene = $self->_prediction();
return $gene;
}
=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, $filehandle) = @_;
my $gene;
my @genes;
#The big parsing loop - parses exons and predicted peptides
while (<$filehandle>)
{
if (/Gene/i)
{
$gene = new Bio::SeqFeature::Generic (
-primary => 'pseudogene',
-source => 'pseudowise');
push @genes, $gene;
while(<$filehandle>) {
my @gene_elements = split;
my $no = scalar(@gene_elements);
if ((/Gene/i) && $no == 3) {
my @element = split;
my $no = scalar(@element);
my $gene_start = $element[1];
my $gene_end = $element[2];
$gene->start($gene_start);
$gene->end($gene_end);
}
elsif (/Exon/i) {
my @element = split;
my $no = scalar(@element);
my $exon_start = $element[1];
my $exon_end = $element[2];
my $exon_phase = $element[4];
my $exon = new Bio::SeqFeature::Generic (
-start => $exon_start,
-end => $exon_end,
-primary => 'exon',
-source => 'pseudowise',
-frame => $exon_phase);
$gene->add_sub_SeqFeature($exon);
}
elsif ((/Gene/i) && $no != 3) {
$gene = new Bio::SeqFeature::Generic (
-primary => 'pseudogene',
-source => 'pseudowise');
push @genes, $gene;
}
}
}
}
$self->_add_prediction(\@genes);
$self->_predictions_parsed(1);
}
=head1 _prediction
Title : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
=cut
sub _prediction {
my ($self) = @_;
return undef unless(exists($self->{'_preds'}) && @{$self->{'_preds'}});
return shift(@{$self->{'_preds'}});
}
=head2 _add_prediction
Title : _add_prediction()
Usage : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :
=cut
sub _add_prediction {
my ($self, $gene) = @_;
if(! exists($self->{'_preds'})) {
$self->{'_preds'} = [];
}
push(@{$self->{'_preds'}}, $gene);
}
=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;
]]>