Raw content of Bio::Tools::Genomewise # $Id: Genomewise.pm,v 1.1.2.1 2003/03/25 12:32:16 heikki Exp $ # # BioPerl module for Bio::Tools::Genomewise # # Copyright Jason Stajich <jason@bioperl.org> # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Tools::Genomewise - Results of one Genomewise run =head1 SYNOPSIS use Bio::Tools::Genomewise; my $gw = Bio::Tools::Genomewise(-file=>"genomewise.out"); while (my $gene = $gw->next_prediction){ my @transcripts = $gw->transcripts; foreach my $t(@transcripts){ my @exons = $t->exons; foreach my $e(@exons){ print $e->start." ".$e->end."\n"; } } } =head1 DESCRIPTION This is the parser for the output of Genewise. It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object. You will need to specify the proper target sequence id on the object with the $feature-E<gt>seq_id($seqid). =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 Email: fugui@worf.fugu-sg.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::Genomewise; use vars qw(@ISA $Srctag); use strict; use Bio::Tools::Genewise; use Bio::Tools::AnalysisResult; use Bio::SeqFeature::Generic; use Bio::SeqFeature::Gene::Exon; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Gene::Transcript; use Bio::SeqFeature::Gene::GeneStructure; @ISA = qw(Bio::Tools::Genewise); $Srctag = 'genomewise'; =head2 new Title : new Usage : $obj->new(-file=>"genewise.out"); $obj->new(-fh=>\*GW); Function: Constructor for genomewise wrapper. Takes either a file or filehandle Example : Returns : L<Bio::Tools::Genomewise> =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 _get_strand Title : _get_strand Usage : $obj->_get_strand Function: takes start and end values, swap them if start>end and returns end Example : Returns :$start,$end,$strand =cut =head2 score Title : score Usage : $obj->score Function: get/set for score info Example : Returns : a score value =cut =head2 _prot_id Title : _prot_id Usage : $obj->_prot_id Function: get/set for protein id Example : Returns :a protein id =cut =head2 _target_id Title : _target_id Usage : $obj->_target_id Function: get/set for genomic sequence id Example : Returns :a target id =cut =head2 next_prediction Title : next_prediction Usage : while($gene = $genewise->next_prediction()) { # do something } Function: Returns the gene structure prediction of the Genomewise result file. Call this method repeatedly until FALSE is returned. Example : Returns : a Bio::SeqFeature::Gene::GeneStructure object Args : =cut sub next_prediction { my ($self) = @_; my $genes; while ($_ = $self->_readline) { $self->debug( $_ ) if( $self->verbose > 0); last if( /^\/\//); if( /^Gene\s+\d+\s*$/ ) { $genes = new Bio::SeqFeature::Gene::GeneStructure (-source => $Srctag, -seq_id => $self->_target_id, # if this had been specified ); $_ = $self->_readline; $self->debug( $_ ) if( $self->verbose > 0); unless ( /^Gene\s+(\d+)\s+(\d+)\s*$/ ) { $self->warn("Unparseable genomewise output"); last; } my $transcript = new Bio::SeqFeature::Gene::Transcript (-source => $Srctag, -seq_id => $self->_target_id, # if this had been specified -start => $1, -end => $2, ); my $nbr = 1; while( $_ = $self->_readline ) { $self->debug( $_ ) if( $self->verbose > 0); unless( m/^\s+Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/ ){ $self->_pushback($_); last; } my ($e_start,$e_end,$phase,$e_strand) = ($1,$2,$3); ($e_start,$e_end,$e_strand) = $self->_get_strand($e_start, $e_end); $transcript->strand($e_strand) unless $transcript->strand != 0; my $exon = new Bio::SeqFeature::Gene::Exon (-seq_id=>$self->_target_id, -source => $Srctag, -start=>$e_start, -end=>$e_end, -frame => $phase, -strand=>$e_strand); $exon->add_tag_value("Exon",$nbr++); $exon->add_tag_value('phase',$phase); $transcript->add_exon($exon); } $genes->add_transcript($transcript); last; # only process a single gene at a time } } return $genes; } 1;