Raw content of Bio::EnsEMBL::ExternalData::Haplotype::Haplotype
<![CDATA[#
# BioPerl module for Bio::EnsEMBL::ExternalData::Haplotype::Haplotype
#
# Cared for by Tony Cox <avc@sanger.ac.uk>
#
# Copyright EnsEMBL
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
HaplotypeAdaptor - DESCRIPTION of Object
This object represents a database of haplotypes.
=head1 SYNOPSIS
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::ExternalData::Haplotype::HaplotypeAdaptor;
use Bio::EnsEMBL::ExternalData::Haplotype::Haplotype;
$hapdb = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-user => 'ensro',
-dbname => 'haplotype_5_28',
-host => 'ecs3d',
-driver => 'mysql',
);
my $hap_adtor = Bio::EnsEMBL::ExternalData::Haplotype::HaplotypeAdaptor->new($hapdb);
$hap = $hap_adtor->get_Haplotype_by_id('B10045'); # Haplotype id
### You can add the HaplotypeAdaptor as an 'external adaptor' to the 'main'
### Ensembl database object, then use it as:
$ensdb = Bio::EnsEMBL::DBSQL::DBAdaptor->new( ... );
$ensdb->add_ExternalAdaptor('haplotype', $hap_adtor);
# then later on, elsewhere:
$hap_adtor = $ensdb->get_ExternalAdaptor('haplotype');
# also available:
$ensdb->list_ExternalAdaptors();
$ensdb->remove_ExternalAdaptor('haplotype');
=head1 DESCRIPTION
This module is an entry point into a database of haplotypes,
The objects can only be read from the database, not written. (They are
loaded ussing a separate perl script).
For more info, see Haplotype.pm
=head1 CONTACT
Tony Cox <Lavc@sanger.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...;
package Bio::EnsEMBL::ExternalData::Haplotype::Haplotype;
use vars qw(@ISA);
use strict;
# Object preamble - inheriets from Bio::Root::Object
use Bio::Root::Object;
@ISA = qw(Bio::Root::Object);
=head2 new
Title : new
Usage : not intended for general use.
Function:
Example :
Returns : a haplotype - caller has to fill using methods
Args :
=cut
sub new {
my ($class, $adaptor) = @_;
my $self = {'_adaptor' => $adaptor};
bless $self,$class;
$self;
}
=head2 id
Title : id
Usage :
Function: get/set the display id of the Haplotype
Example :
Returns :
Args :
=cut
sub id {
my ($self,$value) = @_;
if( defined $value) {
$self->{'id'} = $value;
}
return $self->{'id'};
}
=head2 chr_name
Title : chr_name
Usage :
Function: get/set the chr_name of the Haplotype
Example :
Returns :
Args :
=cut
sub chr_name {
my ($self,$value) = @_;
if( defined $value) {
$self->{'chr_name'} = $value;
}
return $self->{'chr_name'};
}
=head2 contig_id
Title : contig_id
Usage :
Function: get/set the contig id of the Haplotype
Example :
Returns :
Args :
=cut
sub contig_id {
my ($self,$value) = @_;
if( defined $value) {
$self->{'contig_id'} = $value;
}
return $self->{'contig_id'};
}
=head2 start
Title : start
Usage :
Function: get/set the global (chromosomal) start of the Haplotype
Example :
Returns :
Args :
=cut
sub start {
my ($self,$value) = @_;
if( defined $value) {
$self->{'start'} = $value;
}
return $self->{'start'};
}
=head2 end
Title : end
Usage :
Function: get/set the global (chromosomal) end of the Haplotype
Example :
Returns :
Args :
=cut
sub end {
my ($self,$value) = @_;
if( defined $value) {
$self->{'end'} = $value;
}
return $self->{'end'};
}
=head2 local_start
Title : local_start
Usage :
Function: get/set the local (contig) start of the Haplotype
Example :
Returns :
Args :
=cut
sub local_start {
my ($self,$value) = @_;
if( defined $value) {
$self->{'local_start'} = $value;
}
unless ($self->{'local_start'}){
my $id = $self->id();
my $q = qq(
select first_reference_position from block
where block_id = "$id"
);
my $sth = $self->adaptor->prepare($q);
$sth->execute();
($self->{'local_start'}) = $sth->fetchrow_array()
}
return $self->{'local_start'};
}
=head2 local_end
Title : local_end
Usage :
Function: get/set the local (contig) end of the Haplotype
Example :
Returns :
Args :
=cut
sub local_end {
my ($self,$value) = @_;
if( defined $value) {
$self->{'local_end'} = $value;
}
unless ($self->{'local_end'}){
my $id = $self->id();
my $q = qq(
select last_reference_position from block
where block_id = "$id"
);
my $sth = $self->adaptor->prepare($q);
$sth->execute();
($self->{'local_end'}) = $sth->fetchrow_array()
}
return $self->{'local_end'};
}
=head2 snp_req
Title : snp_req
Usage :
Function: get/set the number of SNPs required to unambiguously this Haplotype pattern
Example :
Returns :
Args :
=cut
sub snp_req {
my ($self,$value) = @_;
if( defined $value) {
$self->{'snp_req'} = $value;
}
return $self->{'snp_req'};
}
=head2 snp_info
Title : snp_info
Usage :
Function: get snp_info for names SNP of the Haplotype
Example :
Returns : ref to hash of snp info
Args : read only
=cut
sub snp_info {
my ($self,$value) = @_;
unless ($self->{'snp_info'}->{$value}){
my $q = qq(
select
position,ref_base,alt_base,ref_calls,mut_calls
from
polymorphism
where
polymorphism_id = "$value"
);
my $sth = $self->adaptor->prepare($q);
$sth->execute();
$self->{'snp_info'}->{$value} = $sth->fetchrow_hashref()
}
return $self->{'snp_info'}->{$value};
}
=head2 snps
Title : snps
Usage :
Function: get/set the IDs of SNPs in this Haplotype pattern
Example :
Returns : ref to list of SNP IDs
Args : ref to list of SNP IDs
=cut
sub snps {
my ($self,$value) = @_;
if( defined $value) {
$self->{'snps'} = $value;
}
return $self->{'snps'};
}
=head2 patterns
Title : pattern
Usage :
Function: get/set the sorted list of patterns for this Haplotype consensus
Example :
Returns :
Args :ref to a list of pattern objects (they will be sorted on order of size)
=cut
sub patterns {
my ($self,$value) = @_;
if( defined $value) {
$self->{'patterns'} = $value;
}
my @pats = reverse sort { $a->count <=> $b->count } @{$self->{'patterns'}};
return(\@pats);
}
=head2 adaptor
Title : _adaptor
Usage : $adaptor = $hap->adaptor
Function: find this objects\'s adaptor object (set by HaplotypeAdaptor)
Example :
Returns :
Args :
=cut
sub adaptor {
my ($self)= shift;
return $self->{'_adaptor'};
}
=head2 samples_count
Title : samples_count
Usage :
Function: store number of classified samples
Example :
Returns :
Args :
=cut
sub samples_count {
my ($self,$value) = @_;
if( defined $value) {
$self->{'samples_count'} = $value;
}
return $self->{'samples_count'} ||= 0;
}
=head2 unclassified_samples_count
Title : unclassified_samples_count
Usage :
Function: store number of unclassified samples
Example :
Returns :
Args : ref to a hash of sample=>patterns
=cut
sub unclassified_samples_count {
my ($self,$value) = @_;
if( defined $value) {
$self->{'unclassified_samples_count'} = $value;
}
return $self->{'unclassified_samples_count'} ||= 0;
}
=head2 total_samples
Title : total_samples
Usage :
Function: store total_samples
Example :
Returns :
Args :
=cut
sub total_samples {
my ($self,$value) = @_;
if( defined $value) {
$self->{'total_samples'} = $value;
}
return $self->{'total_samples'} ||= 0;
}
sub fetchSNPs {
my ($self) = @_;
return $self->adaptor->fetchSNPs( $self->id );
}
1;
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