Raw content of Bio::EnsEMBL::TranscriptMapper
<![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
TranscriptMapper - A utility class used to perform coordinate conversions
between a number of coordinate systems relating to transcripts
=head1 SYNOPSIS
my $trmapper = Bio::EnsEMBL::TranscriptMapper->new($transcript);
@coords = $trmapper->cdna2genomic( 123, 554 );
@coords = $trmapper->genomic2cdna( 141, 500, -1 );
@coords = $trmapper->genomic2cds( 141, 500, -1 );
@coords = $trmapper->pep2genomic( 10, 60 );
@coords = $trmapper->genomic2pep( 123, 400, 1 );
=head1 DESCRIPTION
This is a utility class which can be used to perform coordinate conversions
between a number of coordinate systems relating to transcripts.
=head1 METHODS
=cut
package Bio::EnsEMBL::TranscriptMapper;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Mapper::Gap;
use Bio::EnsEMBL::Mapper::Coordinate;
=head2 new
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript for which a TranscriptMapper should be created.
Example : $trans_mapper = Bio::EnsEMBL::TranscriptMapper->new($transcript)
Description: Creates a TranscriptMapper object which can be used to perform
various coordinate transformations relating to transcripts.
Note that the TranscriptMapper uses the transcript state at the
time of creation to perform the conversions, and that a new
TranscriptMapper must be created if the Transcript is altered.
'Genomic' coordinates are coordinates which are relative to the
slice that the Transcript is on.
Returntype : Bio::EnsEMBL::TranscriptMapper
Exceptions : throws if a transcript is not an argument
Caller : Transcript::get_TranscriptMapper
Status : Stable
=cut
sub new {
my $caller = shift;
my $transcript = shift;
my $class = ref($caller) || $caller;
if(!ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript')) {
throw("Transcript argument is required.");
}
# Create a cdna <-> genomic mapper and load it with exon coords
my $mapper = _load_mapper($transcript);
my $exons = $transcript->get_all_Exons();
my $start_phase;
if(@$exons) {
$start_phase = $exons->[0]->phase;
} else {
$start_phase = -1;
}
my $self = bless({'exon_coord_mapper' => $mapper,
'start_phase' => $start_phase,
'cdna_coding_start' => $transcript->cdna_coding_start(),
'cdna_coding_end' => $transcript->cdna_coding_end()},
$class);
}
=head2 _load_mapper
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript for which a mapper should be created.
Example : my $mapper = _load_mapper($transcript);
Description: loads the mapper
Returntype : Bio::EnsEMBL::Mapper
Exceptions : none
Caller : Internal
Status : Stable
=cut
sub _load_mapper {
my $transcript = shift;
my $mapper = Bio::EnsEMBL::Mapper->new( 'cdna', 'genomic');
my $edits_on = $transcript->edits_enabled();
my @edits;
if($edits_on) {
@edits = @{$transcript->get_all_SeqEdits()};
@edits = sort {$a->start() <=> $b->start()} @edits;
}
my $edit_shift = 0;
my $cdna_start = undef;
my $cdna_end = 0;
foreach my $ex (@{$transcript->get_all_Exons}) {
my $gen_start = $ex->start();
my $gen_end = $ex->end();
$cdna_start = $cdna_end + 1;
$cdna_end = $cdna_start + $ex->length() - 1;
my $strand = $ex->strand();
# add deletions and insertions into pairs when SeqEdits turned on
# ignore mismatches (i.e. treat as matches)
if($edits_on) {
while(@edits && $edits[0]->start() + $edit_shift <= $cdna_end) {
my $edit = shift(@edits);
my $len_diff = $edit->length_diff();
if($len_diff) {
# break pair into two parts, finish first pair just before edit
my $prev_cdna_end = $edit->start() + $edit_shift - 1;
my $prev_cdna_start = $cdna_start;
my $prev_len = $prev_cdna_end - $prev_cdna_start + 1;
my $prev_gen_end;
my $prev_gen_start;
if($strand == 1) {
$prev_gen_start = $gen_start;
$prev_gen_end = $gen_start + $prev_len - 1;
} else {
$prev_gen_start = $gen_end - $prev_len + 1;
$prev_gen_end = $gen_end;
}
if($prev_len > 0) { # only create map pair if not boundary case
$mapper->add_map_coordinates
('cdna', $prev_cdna_start, $prev_cdna_end, $strand,
'genome', $prev_gen_start,$prev_gen_end);
}
$cdna_start = $prev_cdna_end + 1;
if($strand == 1) {
$gen_start = $prev_gen_end + 1;
} else {
$gen_end = $prev_gen_start - 1;
}
$cdna_end += $len_diff;
if($len_diff > 0) {
# insert in cdna, shift cdna coords along
$cdna_start += $len_diff;
} else {
# delete in cdna (insert in genomic), shift genomic coords along
if($strand == 1) {
$gen_start -= $len_diff;
} else {
$gen_end += $len_diff;
}
}
$edit_shift += $len_diff;
}
}
}
my $pair_len = $cdna_end - $cdna_start + 1;
if($pair_len > 0) {
$mapper->add_map_coordinates('cdna', $cdna_start, $cdna_end, $strand,
'genome', $gen_start, $gen_end);
}
}
return $mapper;
}
=head2 cdna2genomic
Arg [1] : $start
The start position in cdna coordinates
Arg [2] : $end
The end position in cdna coordinates
Example : @cdna_coords = $transcript_mapper->cdna2genomic($start, $end);
Description: Converts cdna coordinates to genomic coordinates. The
return value is a list of coordinates and gaps.
Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
Bio::EnsEMBL::Mapper::Gap objects
Exceptions : throws if no start or end
Caller : general
Status : Stable
=cut
sub cdna2genomic {
my ($self,$start,$end) = @_;
if( !defined $end ) {
throw("Must call with start/end");
}
my $mapper = $self->{'exon_coord_mapper'};
return $mapper->map_coordinates( 'cdna', $start, $end, 1, "cdna" );
}
=head2 genomic2cdna
Arg [1] : $start
The start position in genomic coordinates
Arg [2] : $end
The end position in genomic coordinates
Arg [3] : $strand
The strand of the genomic coordinates (default value 1)
Example : @coords = $trans_mapper->genomic2cdna($start, $end, $strnd);
Description: Converts genomic coordinates to cdna coordinates. The
return value is a list of coordinates and gaps. Gaps
represent intronic or upstream/downstream regions which do
not comprise this transcripts cdna. Coordinate objects
represent genomic regions which map to exons (utrs included).
Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
Bio::EnsEMBL::Mapper::Gap objects
Exceptions : throws if start, end or strand not defined
Caller : general
Status : Stable
=cut
sub genomic2cdna {
my ($self, $start, $end, $strand) = @_;
unless(defined $start && defined $end && defined $strand) {
throw("start, end and strand arguments are required\n");
}
my $mapper = $self->{'exon_coord_mapper'};
return $mapper->map_coordinates("genome", $start, $end, $strand,"genomic");
}
=head2 pep2genomic
Arg [1] : int $start
start position in peptide coords
Arg [2] : int $end
end position in peptide coords
Example : @genomic_coords = $transcript_mapper->pep2genomic(23, 102);
Description: Converts peptide coordinates into genomic coordinates. The
coordinates returned are relative to the same slice that the
transcript used to construct this TranscriptMapper was on.
Returntype : list of Bio::EnsEMBL::Mapper::Gap and
Bio::EnsEMBL::Mapper::Coordinate objects
Exceptions : throws if no end
Caller : general
Status : Stable
=cut
sub pep2genomic {
my ($self,$start,$end) = @_;
if( !defined $end ) {
throw("Must call with start/end");
}
# move start end into translate cDNA coordinates now.
# much easier!
$start = 3* $start-2 + ($self->{'cdna_coding_start'} - 1);
$end = 3* $end + ($self->{'cdna_coding_start'} - 1);
return $self->cdna2genomic( $start, $end );
}
=head2 genomic2cds
Arg [1] : int $start
The genomic start position
Arg [2] : int $end
The genomic end position
Arg [3] : int $strand
The genomic strand
Example : @cds_coords = $trans_mapper->genomic2cds($start, $end, $strand);
Description: Converts genomic coordinates into CDS coordinates of the
transcript that was used to create this transcript mapper.
Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
Bio::EnsEMBL::Mapper::Gap objects
Exceptions : throw if start, end or strand not defined
Caller : general
Status : Stable
=cut
sub genomic2cds {
my ($self, $start, $end, $strand) = @_;
if(!defined($start) || !defined($end) || !defined($strand)) {
throw("start, end and strand arguments are required");
}
if($start > $end + 1) {
throw("start arg must be less than or equal to end arg + 1");
}
my $cdna_cstart = $self->{'cdna_coding_start'};
my $cdna_cend = $self->{'cdna_coding_end'};
#this is a pseudogene if there is no coding region
if(!defined($cdna_cstart)) {
#return a gap of the entire requested region, there is no CDS
return Bio::EnsEMBL::Mapper::Gap->new($start,$end);
}
my @coords = $self->genomic2cdna($start, $end, $strand);
my @out;
foreach my $coord (@coords) {
if($coord->isa('Bio::EnsEMBL::Mapper::Gap')) {
push @out, $coord;
} else {
my $start = $coord->start;
my $end = $coord->end;
if($coord->strand == -1 || $end < $cdna_cstart || $start > $cdna_cend) {
#is all gap - does not map to peptide
push @out, Bio::EnsEMBL::Mapper::Gap->new($start,$end);
} else {
#we know area is at least partially overlapping CDS
my $cds_start = $start - $cdna_cstart + 1;
my $cds_end = $end - $cdna_cstart + 1;
if($start < $cdna_cstart) {
#start of coordinates are in the 5prime UTR
push @out, Bio::EnsEMBL::Mapper::Gap->new($start, $cdna_cstart-1);
#start is now relative to start of CDS
$cds_start = 1;
}
my $end_gap = undef;
if($end > $cdna_cend) {
#end of coordinates are in the 3prime UTR
$end_gap = Bio::EnsEMBL::Mapper::Gap->new($cdna_cend + 1, $end);
#adjust end to relative to CDS start
$cds_end = $cdna_cend - $cdna_cstart + 1;
}
#start and end are now entirely in CDS and relative to CDS start
$coord->start($cds_start);
$coord->end($cds_end);
push @out, $coord;
if($end_gap) {
#push out the region which was in the 3prime utr
push @out, $end_gap;
}
}
}
}
return @out;
}
=head2 genomic2pep
Arg [1] : $start
The start position in genomic coordinates
Arg [2] : $end
The end position in genomic coordinates
Arg [3] : $strand
The strand of the genomic coordinates
Example : @pep_coords = $transcript->genomic2pep($start, $end, $strand);
Description: Converts genomic coordinates to peptide coordinates. The
return value is a list of coordinates and gaps.
Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
Bio::EnsEMBL::Mapper::Gap objects
Exceptions : throw if start, end or strand not defined
Caller : general
Status : Stable
=cut
sub genomic2pep {
my ($self, $start, $end, $strand) = @_;
unless(defined $start && defined $end && defined $strand) {
throw("start, end and strand arguments are required");
}
my @coords = $self->genomic2cds($start, $end, $strand);
my @out;
my $start_phase = $self->{'start_phase'};
#take into account possible N padding at beginning of CDS
my $shift = ($start_phase > 0) ? $start_phase : 0;
foreach my $coord (@coords) {
if($coord->isa('Bio::EnsEMBL::Mapper::Gap')) {
push @out, $coord;
} else {
#start and end are now entirely in CDS and relative to CDS start
#convert to peptide coordinates
my $pep_start = int(($coord->start + $shift + 2) / 3);
my $pep_end = int(($coord->end + $shift + 2) / 3);
$coord->start($pep_start);
$coord->end($pep_end);
push @out, $coord;
}
}
return @out;
}
1;
]]>