Raw content of Bio::EnsEMBL::ExternalData::Disease::DiseaseLocation
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# BioPerl module for Bio::EnsEMBL::ExternalData::Disease::DiseaseLocation
#
# Written by Arek Kasprzyk <arek@ebi.ac.uk>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::ExternalData::Disease::Disease
=head1 SYNOPSIS
my $location=new Bio::EnsEMBL::ExternalData::Disease::DiseaseLocation(
-db_id=>$rowhash->{'omim_id'},
-cyto_start=>$rowhash->{'start_cyto'},
-cyto_end=>$rowhash->{'end_cyto'},
-external_gene=>$rowhash->{'gene_symbol'},
-chromosome=>$rowhash->{'chromosome'});
=head1 DESCRIPTION
This object holds info about genomic location of a disease phenotype
=head1 AUTHOR - Arek Kasprzyk
Email arek@ebi.ac.uk
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::ExternalData::Disease::DiseaseLocation;
use strict;
use Bio::EnsEMBL::Root;
use vars qw(@ISA);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
@ISA = qw(Bio::EnsEMBL::Root);
=head2 new
Title : new
Usage : see DBHandler's fetch methods
=cut
sub new
{
my($class,@args) = @_;
my $self = bless {}, $class;
my ($db_id,$cyto_start,$cyto_end,$gene_id,$chromosome) =
rearrange([qw(
DB_ID
CYTO_START
CYTO_END
EXTERNAL_GENE
CHROMOSOME
)],@args);
# $db_id || $self->throw("I need external db id");
# $cyto_start || $self->throw("I need cytogenetic position ");
# $cyto_end || $self->throw("I need cytogenetic position");
$self->db_id($db_id);
$self->cyto_start($cyto_start);
$self->cyto_end($cyto_end);
if (defined $chromosome){$self->chromosome($chromosome);}
if (defined $gene_id){$self->external_gene($gene_id);}
return $self;
}
=head2 db_id
Title : db_id
Usage :
Function: Get/set the omim_id from NCBI, not the id in the disease table!
Example :
Returns :
Args :
=cut
sub db_id
{
my ($self,$value) = @_;
if( defined $value) {$self->{'_db_id'} = $value;}
return $self->{'_db_id'};
}
=head2 has_gene
Title : has_gene
Usage :
Function:
Example :
Returns :
Args :
=cut
sub has_gene
{
my ($self,$value) = @_;
if( defined $value) {$self->{'_has_gene'} = $value;}
return $self->{'_has_gene'};
}
=head2 external_gene
Title : external_gene
Usage :
Function: Get/Set the gene_symbol, same as in NCBI OMIM, for human.
Example :
Returns :
Args :
=cut
sub external_gene
{
my ($self,$value) = @_;
if( defined $value) {$self->{'_gene_id'} = $value;}
return $self->{'_gene_id'};
}
=head2 ensembl_gene
Title : ensembl_gene
Usage :
Function:
Example :
Returns :
Args :
=cut
sub ensembl_gene
{
my ($self,$value) = @_;
if( defined $value) {$self->{'ensembl_gene'} = $value;}
return $self->{'ensembl_gene'};
}
=head2 cyto_start
Title : cyto_start
Usage :
Function:
Example :
Returns :
Args :
=cut
sub cyto_start
{
my ($self,$value) = @_;
if( defined $value) {$self->{'_cyto_start'} = $value;}
return $self->{'_cyto_start'};
}
=head2 cyto_end
Title : cyto_end
Usage :
Function:
Example :
Returns :
Args :
=cut
sub cyto_end
{
my ($self,$value) = @_;
if( defined $value) {$self->{'_cyto_end'} = $value;}
return $self->{'_cyto_end'};
}
=head2 chromosome
Title : chromosome
Usage :
Function: Get/set the chromosome name. X is 'X', not 23!
Example :
Returns :
Args :
=cut
sub chromosome
{
my ($self,$value) = @_;
if( defined $value) {$self->{'chromosome'} = $value;}
return $self->{'chromosome'};
}
=head2 global_position
Title : global_position
Usage :
Function:
Example :
Returns :
Args :
=cut
sub global_position
{
my ($self,$value) = @_;
if( defined $value) {$self->{'global_position'} = $value;}
return $self->{'global_position'};
}
1;
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