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Bio-EnsEMBL-113.0.0
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/ Bio::EnsEMBL::DBSQL::GenomeContainer

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

NAME

NAME

Bio::EnsEMBL::DBSQL::GenomeContainer - Encapsulates all access to genome related information

SYNOPSIS

use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_db(
  -host => 'ensembldb.ensembl.org',
  -user => 'anonymous'
);

$genome =
  Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "GenomeContainer" );

my $version = $genome->get_version;

my $ref_length = $genome->get_ref_length;

my $coord_systems = $genome->get_coord_systems;

DESCRIPTION

This module is responsible for fetching and storing genome-wide information. Genome is an abstract object which contains information linking the species, the assembly and the ensembl annotation.

METHODS

new

Arg [...]  : Superclass args.  See Bio::EnsEMBL::DBSQL::BaseAdaptor
Description: Instantiates a Bio::EnsEMBL::DBSQL::GenomeContainer
Returntype : Bio::EnsEMBL::GenomeContainer
Exceptions : none
Caller     : DBAdaptor
Status     : Stable

store

Arg [1]    : Statistic
             The type of statistic to store
Arg [2]    : Value
             The corresponding value for the statistic
Arg [3]    : (optional) Attribute
             If more than one value exists for the statistics, it will be distinguished by its attribute
Example    : $genome_adaptor->store('coding_cnt', 20769);
Description: Stores a genome statistic in the database
Returntype : The database identifier (dbID) of the newly stored genome statistic
Exceptions :
Caller     : general
Status     : Stable

update

Arg [1]    : Statistic
             The type of statistic to update
Arg [2]    : Value
             The corresponding value for the statistic
Arg [3]    : (optional) Attribute
             If more than one value exists for the statistics, it will be distinguished by its attribute
Example    : $genome_adaptor->update('coding_cnt', 20769);
Description: Updates an existing genome statistic in the database
Returntype : none
Exceptions :
Caller     : general
Status     : Stable

_meta_container

Arg [1]    : none
Example    : $meta_container = $genome->_meta_container();
Description: Internal method to return a MetaContainer object for the genome
Returntype : Bio::EnsEMBL::DBSQL::MetaContainer
Exceptions : none
Caller     : general
Status     : Stable

get_version

Arg [1]    : (optional) assembly version
Example    : $version = $genome->get_version();
Description: Getter/Setter for the assembly version

Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

get_accession

Arg [1]    : (optional) assembly accession
Example    : $accession = $genome->get_accession();
Description: Getter/setter for the accession of the assembly currently used

Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

get_assembly_name

Arg [1]    : (optional) assembly name
Example    : $assembly_name = $genome->get_assembly_name();
Description: Getter/setter for the name of the assembly currently used

Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

get_assembly_date

Arg [1]    : (optional) assembly date
Example    : $assembly_date = $genome->get_assembly_date();
Description: Getter/setter for the date of the assembly currently used

Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

get_genebuild_start_date

Arg [1]    : (optional) genebuild start date
Example    : $genebuild_start_date = $genome->get_genebuild_start_date();
Description: Getter/setter for the start date of the genebuild currently used

Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

get_genebuild_method

Arg [1]    : (optional) genebuild start date
Example    : $genebuild_method = $genome->get_genebuild_method();
Description: Getter/setter for the method of the genebuild currently used

Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

get_genebuild_initial_release_date

Arg [1]    : (optional) genebuild initial release date
Example    : $genebuild_initial_release_date = $genome->get_initial_release_date();
Description: Getter/setter for the initial release date of the genebuild currently used

Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

get_genebuild_last_geneset_update

Arg [1]    : (optional) genebuild last geneset update
Example    : $genebuild_last_geneset_update = $genome->get_last_geneset_update();
Description: Getter/setter for the last geneset update of the genebuild currently used

Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

_get_length

Arg [1]    : none
Example    : $length = $genome->_get_length('toplevel');
Description: Internal method to return the length for a type of slices
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_ref_length

Arg [1]    : (optional) golden path length
Example    : $ref_length = $genome->get_ref_length();
Description: Getter/setter for the golden path of the assembly currently used
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_toplevel

Arg [1]    : none
Example    : $toplevel = $genome->get_toplevel();
Description: Returns the toplevel for the assembly currently used

Returntype : ListRef of Bio::EnsEMBL::Slice
Exceptions : none
Caller     : general
Status     : Stable

get_karyotype

Arg [1]    : none
Example    : $karyotype = $genome->get_karyotype();
Description: Returns the karyotype for the assembly currently used

Returntype : ListRef of Bio::EnsEMBL::Slice
Exceptions : none
Caller     : general
Status     : Stable

get_coord_systems

Arg [1]    : none
Example    : $coord_systems = $genome->get_coord_systems();
Description: Returns the coord_systems for the assembly currently used

Returntype : ListRef of Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller     : general
Status     : Stable

_get_count

Arg [1]    : none
Example    : $count = $genome->_get_count('coding_cnt');
Description: Internal method to return a count for a given attribute code
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_count

Arg [1]    : none
Example    : $count = $genome->get_count('coding_cnt');
Description: Retrieve a count for a given attribute code
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

fetch_all_statistics

Arg [1]    : none
Example    : $list = $genome->fetch_all_statistics();
Description: Retrieve all entries stored in the genome_statistics table
Returntype : ArrayRef of Bio::EnsEMBL::Genome
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_statistic

Arg [1]    : string $statistic
Example    : $results = $genome->fetch_by_statistic('coding_cnt');
Description: Returns a Genome object for a given statistic
Returntype : Bio::EnsEMBL::Genome
Exceptions : none
Caller     : general
Status     : Stable

is_empty

Arg [1]    : none
Example    : $results = $genome->is_empty;
Description: Boolean to check if there is data in the genome container
Returntype : Boolean
Exceptions : none
Caller     : general
Status     : Stable

get_attrib

Arg [1]    : statistic
Example    : $results = $genome->_get_attrib('coding_cnt');
Description: Returns the attribute object for a given statistic
Returntype : Bio::EnsEMBL::Attrib
Exceptions : none
Caller     : general
Status     : Stable

get_coding_count

Arg [1]    : (optional) coding count
Example    : $coding_count = $genome->get_coding_count();
Description: Getter/setter for the number of coding genes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_rcoding_count

Arg [1]    : (optional) readthrough coding count
Example    : $rcoding_count = $genome->get_rcoding_count();
Description: Getter/setter for the number of readthrough coding genes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_snoncoding_count

Arg [1]    : (optional) short non coding count
Example    : $snoncoding_count = $genome->get_snoncoding_count();
Description: Getter/setter for the number of short non coding genes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_rsnoncoding_count

Arg [1]    : (optional) readthrough short non coding count
Example    : $rsnoncoding_count = $genome->get_rsnoncoding_count();
Description: Getter/setter for the number of readthrough short non coding genes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_mnoncoding_count

Arg [1]    : (optional) miscellaneous non coding count
Example    : $mnoncoding_count = $genome->get_mnoncoding_count();
Description: Getter/setter for the number of miscellaneous non coding genes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_rmnoncoding_count

Arg [1]    : (optional) readthrough miscellaneous non coding count
Example    : $rmnoncoding_count = $genome->get_rmnoncoding_count();
Description: Getter/setter for the number of readthrough miscellaneous non coding genes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_lnoncoding_count

Arg [1]    : (optional) long non coding count
Example    : $lnoncoding_count = $genome->get_lnoncoding_count();
Description: Getter/setter for the number of long non coding genes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_rlnoncoding_count

Arg [1]    : (optional) readthrough long non coding count
Example    : $rlnoncoding_count = $genome->get_rlnoncoding_count();
Description: Getter/setter for the number of readthrough long non coding genes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_pseudogene_count

Arg [1]    : (optional) pseudogene count
Example    : $pseudogene_count = $genome->get_pseudogene_count();
Description: Getter/setter for the number of pseudogenes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_rpseudogene_count

Arg [1]    : (optional) readthrough pseudogene count
Example    : $rpseudogene_count = $genome->get_rpseudogene_count();
Description: Getter/setter for the number of readthrough pseudogenes in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_coding_count

Arg [1]    : (optional) alt coding count
Example    : $alt_coding_count = $genome->get_alt_coding_count();
Description: Getter/setter for the number of coding genes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_rcoding_count

Arg [1]    : (optional) alt readthrough coding count
Example    : $alt_rcoding_count = $genome->get_alt_rcoding_count();
Description: Getter/setter for the number of readthrough coding genes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_snoncoding_count

Arg [1]    : (optional) alt short non coding count
Example    : $alt_snoncoding_count = $genome->get_alt_snoncoding_count();
Description: Getter/setter for the number of short non coding genes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_rsnoncoding_count

Arg [1]    : (optional) alt readthrough short non coding count
Example    : $alt_rsnoncoding_count = $genome->get_alt_rsnoncoding_count();
Description: Getter/setter for the number of readthrough short non coding genes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_mnoncoding_count

Arg [1]    : (optional) alt miscellaneous non coding count
Example    : $alt_mnoncoding_count = $genome->get_alt_mnoncoding_count();
Description: Getter/setter for the number of miscellaneous non coding genes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_rmnoncoding_count

Arg [1]    : (optional) alt readthrough miscellaneous non coding count
Example    : $alt_rmnoncoding_count = $genome->get_alt_rmnoncoding_count();
Description: Getter/setter for the number of readthrough miscellaneous non coding genes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_lnoncoding_count

Arg [1]    : (optional) alt long non coding count
Example    : $alt_lnoncoding_count = $genome->get_alt_lnoncoding_count();
Description: Getter/setter for the number of long non coding genes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_rlnoncoding_count

Arg [1]    : (optional) alt readthrough long non coding count
Example    : $alt_lnoncoding_count = $genome->get_alt_lnoncoding_count();
Description: Getter/setter for the number of readthrough long non coding genes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_pseudogene_count

Arg [1]    : (optional) alt pseudogene count
Example    : $alt_pseudogene_count = $genome->get_alt_pseudogene_count();
Description: Getter/setter for the number of pseudogenes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_rpseudogene_count

Arg [1]    : (optional) alt readthrough pseudogene count
Example    : $alt_rpseudogene_count = $genome->get_alt_pseudogene_count();
Description: Getter/setter for the number of readthrough pseudogenes on alternate sequences

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_short_variation_count

Arg [1]    : (optional) short variation count
Example    : $short_variation_count = $genome->get_short_variation_count();
Description: Getter/setter for the number of short variants in the current build

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_prediction_count

Arg [1]    : (optional) logic_name
Example    : $prediction_count = $genome->get_prediction_count();
Description: Getter for the number of predicted genes in the current build
             Can be restricted to a given analysis

Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_structural_variation_count

Arg [1]    : none
Example    : $structural_variation_count = $genome->get_structural_variation_count();
Description: Return the number of structural variations in the current build
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_transcript_count

Arg [1]    : (optional) transcript count
Example    : $transcript_count = $genome->get_transcript_count();
Description: Getter/setter for the number of transcripts in the current build
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_alt_transcript_count

Arg [1]    : (optional) alt transcript count
Example    : $alt_transcript_count = $genome->get_alt_transcript_count();
Description: Getter/setter for the number of transcripts on alternate sequences in the current build
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

has_karyotype

Arg        : None
Example    : $has_karyotype = $genome->has_karyotype();
Description: Boolean indicating whether a genome has a karyotype (ie chromosomes)
             or not
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

is_high_coverage

Arg        : None
Example    : $is_high_coverage = $genome->is_high_coverage();
Description: Boolean indicating whether an assembly is high coverage
             or not
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

is_polyploid

Arg        : None
Example    : $is_polyploid = $genome->is_polyploid();
Description: Returns whether the genome is or is not polyploid.
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

get_genome_components

Arg        : None
Example    : $components = $genome->get_genome_components();
Description: Returns the list of (diploid) components, for a
             polyploid genome
Returntype : Arrayref
Exceptions : none
Caller     : general
Status     : Stable