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lib/Bio/EnsEMBL/TranscriptFactory.pm  view on Meta::CPAN

        
    my @exons;
    my $count= 1;
    
    foreach my $f ($genscan->sub_SeqFeature) {
  
	my $exon  = new Bio::EnsEMBL::Exon;
	$transcript->add_Exon($exon);
        $exon->contig   ($contig);
	$exon->start    ($f->start);
	$exon->end      ($f->end  );
	$exon->strand   ($f->strand);
	$exon->phase    ($f->phase);
	$exon->end_phase( ($exon->phase + $exon->length)%3 );
	#$exon->score($f->score);
#	$exon->p_value($f->p_value);
	$exon->slice($contig->primary_seq);
	
	push(@exons,$exon);
	$count++;
	
    }
    
    if( $count == 1 ) {
	$genscan->throw("Got a 0 exon genscan");
    }

    my $translation = new Bio::EnsEMBL::Translation;
    #
    # This code got changed due to Translation convention changing. Should work...
    #
    
    if ($exons[0]->strand == 1) {
	@exons = sort {$a->start <=> $b->start} @exons;
    } else {
	@exons = sort {$b->start <=> $a->start} @exons;
    }
    
    $translation->start(1);
    $translation->end($exons[scalar(@exons)-1]->length);
    
    $translation->start_Exon($exons[0]);
    $translation->end_Exon($exons[$#exons]);

    my $endphase = $exons[0]->end_phase;
    
    foreach my $exon (@exons) {
	
      if ( $exon == $exons[0] ){
	next;
      }
      $exon->phase         ($endphase);
      $endphase = $exon->end_phase;
    }
    
    $transcript->translation($translation);
    
    return $transcript;
}

sub fset2transcript_guess_phases {
    my ($fset,$contig) = @_;

    my $transcript = new Bio::EnsEMBL::Transcript;

    $transcript->temporary_id($contig->id . "." . $fset->id);


    my @exons;
    my $count    = 1;

    foreach my $f ($fset->sub_SeqFeature) {

	my $exon  = new Bio::EnsEMBL::Exon;
        $exon->contig   ($contig);
	$exon->start    ($f->start);
	$exon->end      ($f->end  );
	$exon->strand   ($f->strand);
	#$exon->score($f->score);
#	$exon->p_value($f->p_value);
	$exon->slice($contig);
	$exon->phase($f->phase); 
	push(@exons,$exon);
	$count++;
	
    }
	
    my $translation = new Bio::EnsEMBL::Translation;
	
    if ($exons[0]->strand == 1) {
	@exons = sort {$a->start <=> $b->start} @exons;
    } else {
	@exons = sort {$b->start <=> $a->start} @exons;
    }
	
    $translation->start        (1);
    $translation->end          ($exons[$#exons]->end - $exons[$#exons]->start + 1);
    $translation->start_Exon($exons[0]);
    $translation->end_Exon($exons[$#exons]);
    $transcript->translation($translation);
    
    my $endphase = 0;
    
    foreach my $exon (@exons) {
	
	$exon      ->phase   ($endphase);
	$transcript->add_Exon($exon);

	$endphase = $exon->end_phase(($exon->phase + $exon->length)%3);
	
    }


    if ($transcript->translate->seq !~ /\*/) {
	return $transcript;
    }  	

    $endphase = 1;
    
    foreach my $exon (@exons) {
	$exon->phase($endphase);