Raw content of Bio::Tools::Pseudowise # 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;