Raw content of Bio::EnsEMBL::TranscriptFactory
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::TranscriptFactory - Module having the fset2transcript*
subroutines
=head1 SYNOPSIS
use Bio::EnsEMBL::TranscriptFactory;
&Bio::EnsEMBL::TranscriptFactory::fset2transcript($fset_id);
=head1 DESCRIPTION
Module containing the subroutines fset2transcript*,
which create transcripts from features (formally housed in
Bio::EnsEMBL::DBSQL::Utils).
=head1 METHODS
=cut
package Bio::EnsEMBL::TranscriptFactory;
use strict;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Translation;
use Bio::EnsEMBL::Transcript;
sub fset2transcript {
my ($genscan,$contig)=@_;
unless ($genscan->isa ("Bio::EnsEMBL::SeqFeatureI"))
{print "$genscan must be Bio::EnsEMBL::SeqFeatureI\n";}
my $transcript = new Bio::EnsEMBL::Transcript;
$transcript->temporary_id($contig->id . "." . $genscan->seqname);
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);
$endphase = $exon->end_phase(($exon->phase + $exon->length)%3);
}
if ($transcript->translate->seq !~ /\*/) {
return $transcript;
}
$endphase = 2;
foreach my $exon (@exons) {
$exon->phase($endphase);
$endphase = $exon->end_phase(($exon->phase + $exon->length)%3);
}
if ($transcript->translate->seq !~ /\*/) {
return $transcript;
}
}
sub fset2transcript_3frame {
my ($fset,$contig) = @_;
my @f = $fset->sub_SeqFeature;
if ($f[0]->strand == 1) {
@f = sort {$a->start <=> $b->start} @f;
} else {
@f = sort {$b->start <=> $a->start} @f;
}
my @transcripts;
my $startphase = 0;
while ($startphase < 3) {
my $endphase = $startphase;
my $transcript = new Bio::EnsEMBL::Transcript;
push(@transcripts,$transcript);
$transcript->temporary_id($contig->id . "." . $endphase);
my $count = 1;
my @exons;
foreach my $f (@f) {
#print "exon seqname = ".$f->seqname."\n";
my $exon = new Bio::EnsEMBL::Exon;
#print STDERR "exon ".$f->gffstring."\n";
push(@exons,$exon);
$exon->seqname($f->seqname);
$exon->temporary_id ($contig->id . ".$count");
$exon->contig ($contig);
$exon->start ($f->start);
$exon->end ($f->end );
$exon->strand ($f->strand);
$exon->slice($contig);
$exon->phase ($endphase);
$exon->end_phase( ($exon->phase + $exon->length)%3 );
#$exon->score ($f->score);
# $exon->p_value ($f->p_value);
$endphase = $exon->end_phase;
$transcript->add_Exon($exon);
$count++;
#print STDERR "Added exon start " . $exon->start . " end " . $exon->end . " strand " . $exon->strand . " score " . $exon->score . " pvalue " . $exon->p_value . "\n";
}
my $translation = new Bio::EnsEMBL::Translation;
my $contig_id = "";
my $fset_id = "";
if (defined($contig->id)) {
$contig_id = $contig->id;
}
if (defined($fset->id)) {
$fset_id = $fset->id;
}
$translation->temporary_id($contig_id . "." . $fset_id);
$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);
# print STDERR "Phase $startphase " . $transcript->translate->seq . "\n";
$startphase++;
}
#print "finshed fset2transcript_3frame\n";
return @transcripts;
}
sub fset2transcript_with_seq {
my ($genscan,$seq)=@_;
unless ($genscan->isa ("Bio::EnsEMBL::SeqFeatureI"))
{print "$genscan must be Bio::EnsEMBL::SeqFeatureI\n";}
unless ($seq->isa ("Bio::PrimarySeqI") || $seq->isa ("Bio::SeqI"))
{print "$seq must be Bio::SeqI or a Bio::PrimarySeqI\n";}
#print STDERR "running fset2transcript\n";
my $transcript = new Bio::EnsEMBL::Transcript;
$transcript->temporary_id($seq->id . "." . $genscan->seqname);
my @exons;
my $count= 1;
foreach my $f ($genscan->sub_SeqFeature) {
my $exon = new Bio::EnsEMBL::Exon;
$exon->contig ($seq);
$exon->start ($f->start);
$exon->end ($f->end );
$exon->strand ($f->strand);
$exon->phase ($f->phase);
$exon->end_phase( ($exon->phase + $exon->length)%3 );
#$exon->score ($f->score);
#print STDERR "contig is a = ".$seq."\n";
$exon->slice($seq);
push(@exons,$exon);
$count++;
}
foreach my $exon (@exons) {
$transcript->add_Exon($exon);
}
return $transcript;
}
1;
]]>