Raw content of Bio::EnsEMBL::ExternalData::DAS::GenomicPeptideMapper
<![CDATA[# Proxy object to adapt TranscriptMapper genomic2pep and pep2genomic methods
# to the core Mapper interface.
# Differences:
# TranscriptMapper uses different named methods to do conversions rather than
# having a Mapper per pair of coordinate systems.
# Transcript Mapper uses slice-relative coordinates...
package Bio::EnsEMBL::ExternalData::DAS::GenomicPeptideMapper;
use strict;
use warnings;
use Bio::EnsEMBL::TranscriptMapper;
use base qw(Bio::EnsEMBL::Mapper);
sub new {
my ( $proto, $from, $to, $from_cs, $to_cs, $transcript ) = @_;
my $class = ref $proto || $proto;
my $self = {
'_mapper' => Bio::EnsEMBL::TranscriptMapper->new( $transcript->transfer($transcript->slice->seq_region_Slice) ),
'from' => $from,
'to' => $to,
'from_cs' => $from_cs,
'to_cs' => $to_cs,
};
bless $self, $class;
my $is_forward = $to_cs->name =~ m/peptide/;
$self->{'genomic_id'} = $transcript->slice->seq_region_name;
$self->{'peptide_id'} = $transcript->translation->stable_id;
$self->{'genomic'} = $is_forward ? $from : $to;
$self->{'peptide'} = $is_forward ? $to : $from;
$self->{'genomic_cs'} = $is_forward ? $from_cs : $to_cs;
$self->{'peptide_cs'} = $is_forward ? $to_cs : $from_cs;
return $self;
}
sub map_coordinates {
my $self = shift;
my (@coords, $out_id, $out_cs);
# Query is genomic
if ( $_[4] eq $self->{'genomic'} ) {
@coords = $self->{'_mapper'}->genomic2pep(@_[1 .. 3]);
$out_id = $self->{'peptide_id'};
$out_cs = $self->{'peptide_cs'};
# Query is peptide
} elsif ( $_[4] eq $self->{'peptide'} ) {
@coords = $self->{'_mapper'}->pep2genomic(@_[1 .. 2]);
$out_id = $self->{'genomic_id'};
$out_cs = $self->{'genomic_cs'};
} else {
throw($_[4].' is neither the genomic or peptide coordinate system');
}
for my $c ( @coords ) {
if ($c->isa('Bio::EnsEMBL::Mapper::Coordinate')) {
$c->id( $out_id );
$c->coord_system( $out_cs ); # TranscriptMapper doesn't set this
}
}
return @coords;
}
1;]]>