Inheritance diagram for Bio::EnsEMBL::MetaData::GenomeInfo:

Class Summary

Synopsis

  my $genome = Bio::EnsEMBL::MetaData::GenomeInfo->new(
      -species    => $dba->species(),
      -species_id => $dba->species_id(),
      -division   => $meta->get_division() || 'Ensembl',
      -dbname     => $dbname);
      
  print Dumper($genome->to_hash());

Description

Object encapsulating meta information about a genome in Ensembl Genomes. 

Can be used to render information about a genome e.g.

print $genome->name()." (".$genome->species.")\n";
print "Sequences: ".scalar(\@{$genome->sequences()})."\n";
if($genome->has_variations()) {
	print "Variations: \n";
	# variations is a hash with type as the key
	while(my ($type,$value) = each %{$genome->variations()}) {
		print "- $type\n";
	}
}
print "Compara analyses: ".scalar(\@{$genome->compara()})."\n";

See-also

Bio::EnsEMBL::MetaData::BaseInfo Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Bio::EnsEMBL::MetaData::GenomeOrganismInfo Bio::EnsEMBL::MetaData::GenomeComparaInfo Bio::EnsEMBL::MetaData::DataReleaseInfo Bio::EnsEMBL::MetaData::DatabaseInfo Bio::EnsEMBL::MetaData::EventInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor

Definition at line 50 of file GenomeInfo.pm.

Available Methods
protected	_get_core ()
protected void	_load_child ()
protected void	_preload ()
protected	_unload ()
public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor	adaptor ()
public String	add_database ()
public Arrayref	aliases ()
public Hashref	annotations ()
public Bio::EnsEMBL::MetaData::GenomeAssemblyInfo	assembly ()
public String	assembly_accession ()
public String	assembly_level ()
public String	assembly_name ()
public Int	base_count ()
public Arrayref	compara ()
public Int	count_alignments ()
public Int	count_hash_lengths ()
public Int	count_hash_values ()
public Int	count_variation ()
public Bio::EnsEMBL::MetaData::DataReleaseInfo	data_release ()
public	databases ()
public String	db_size ()
public DbID	dbID ()
public	dbname ()
public String	display_name ()
public String	division ()
public Hashref	features ()
public String	genebuild ()
public Uniprot	get_uniprot_coverage ()
public Boolean	has_genome_alignments ()
public Boolean	has_other_alignments ()
public Boolean	has_pan_compara ()
public Boolean	has_peptide_compara ()
public Boolean	has_synteny ()
public	has_variations ()
public Bool	is_reference ()
public String	name ()
public	new ()
public Bio::EnsEMBL::MetaData::GenomeOrganismInfo	organism ()
public Hashref	other_alignments ()
public Arrayref	publications ()
public Arrayref	sequences ()
public String	serotype ()
public String	species_id ()
public String	species_taxonomy_id ()
public String	strain ()
public String	taxonomy_id ()
public Hashref	to_hash ()
public String	to_string ()
public Arrayref	variations ()

Method Documentation

protected Bio::EnsEMBL::MetaData::GenomeInfo::_get_core ( )

Undocumented method

Code:

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protected void Bio::EnsEMBL::MetaData::BaseInfo::_load_child ( ) [inherited]

  Description: Lazy load method for loading children from database if not initialised
  Arg        : Key to find child data in object hash
  Arg        : Method for loading child data from adaptor()
  Returntype : none
  Exceptions : none
  Caller     : Internal
  Status     : Stable

Code:

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protected void Bio::EnsEMBL::MetaData::GenomeInfo::_preload ( )

  Description: Ensure all children are loaded (used for hash transformation)
  Returntype : none
  Exceptions : none
  Caller     : Internal
  Status     : Stable

Code:

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  Description: Remove all children (used after hash transformation to ensure object is minimised)
  Returntype : none
  Exceptions : none
  Caller     : dump_metadata.pl
  Status     : Stable

/**

Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

protected Bio::EnsEMBL::MetaData::GenomeInfo::_unload ( )

Undocumented method

Code:

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Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor Bio::EnsEMBL::MetaData::GenomeInfo::adaptor ( )

  Arg        : (optional) adaptor to set set
  Description: Gets/sets GenomeInfoAdaptor
  Returntype : Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor
  Exceptions : none
  Caller     : Internal
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public String Bio::EnsEMBL::MetaData::GenomeInfo::add_database ( )

  Arg        : Name of database
  Arg        : (Optional) species_id (defaults to 1)
  Description: Add a database associated with this genome
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Arrayref Bio::EnsEMBL::MetaData::GenomeInfo::aliases ( )

  Description: Gets aliases by which the genome is also known 
  Returntype : Arrayref of aliases
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Hashref Bio::EnsEMBL::MetaData::GenomeInfo::annotations ( )

  Arg        : (optional) annotations to set
  Description: Gets/sets summary information about gene annotation as hashref, with
  			   annotation type as key and count as value
  Returntype : hashref
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Bio::EnsEMBL::MetaData::GenomeInfo::assembly ( )

  Arg        : (optional) assembly to set
  Description: Gets/sets assembly object
  Returntype : Bio::EnsEMBL::MetaData::GenomeAssemblyInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::assembly_accession ( )

  Description: Gets INSDC accession for assembly
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::assembly_level ( )

  Description: Gets highest level of assembly (chromosome, supercontig etc.)
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::assembly_name ( )

  Description: Gets name of assembly
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Int Bio::EnsEMBL::MetaData::GenomeInfo::base_count ( )

  Description: Gets total number of bases in assembled genome
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Arrayref Bio::EnsEMBL::MetaData::GenomeInfo::compara ( )

  Arg        : (optional) arrayref of GenomeComparaInfo objects to set
  Description: Gets/sets GenomeComparaInfo describing comparative analyses applied to the genome
  Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeComparaInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Int Bio::EnsEMBL::MetaData::GenomeInfo::count_alignments ( )

  Description: Returns total number of alignments to genome
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Int Bio::EnsEMBL::MetaData::GenomeInfo::count_hash_lengths ( )

  Description: Sums sizes of arrays found in hash as values
  Arg		 : hashref
  Returntype : integer
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public Int Bio::EnsEMBL::MetaData::GenomeInfo::count_hash_values ( )

  Description: Sums values found in hash
  Arg		 : hashref
  Returntype : integer
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public Int Bio::EnsEMBL::MetaData::GenomeInfo::count_variation ( )

  Description: Returns total number of variations and structural variations mapped to genome
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::MetaData::DataReleaseInfo Bio::EnsEMBL::MetaData::GenomeInfo::data_release ( )

  Arg        : (optional) Arrayref of DatabaseInfo objects to set
  Description: Gets/sets databases associated with the genome
  Returntype : Arrayref of Bio::EnsEMBL::MetaData::DatabaseInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

/**

  Arg        : (optional) data_release object to set
  Description: Gets/sets data_release to which genome belongs
  Returntype : Bio::EnsEMBL::MetaData::DataReleaseInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::MetaData::GenomeInfo::databases ( )

Undocumented method

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::db_size ( )

  Arg        : (optional) db_size to set
  Description: Gets/sets size of database containing core
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public DbID Bio::EnsEMBL::MetaData::GenomeInfo::dbID ( )

  Arg        : (optional) dbID to set set
  Description: Gets/sets internal genome_id used as database primary key
  Returntype : dbID string
  Exceptions : none
  Caller     : Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public Bio::EnsEMBL::MetaData::GenomeInfo::dbname ( )

Undocumented method

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::display_name ( )

  Description: Gets readable name
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::division ( )

  Arg        : (optional) division to set
  Description: Gets/sets Ensembl Genomes division
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Hashref Bio::EnsEMBL::MetaData::GenomeInfo::features ( )

  Arg        : (optional) features to set
  Description: Gets/sets general genomic features associated with the genome as hashref
  			   keyed by type (e.g. repeatFeatures,simpleFeatures), further broken down into
  			   counts by analysis
  Returntype : Hashref
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::genebuild ( )

  Arg        : (optional) genebuild to set
  Description: Gets/sets identifier for genebuild
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Uniprot Bio::EnsEMBL::MetaData::GenomeInfo::get_uniprot_coverage ( )

  Description: Get % of protein coding genes with a UniProt cross-reference
  Returntype : uniprot coverage as percentage
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Boolean Bio::EnsEMBL::MetaData::GenomeInfo::has_genome_alignments ( )

  Arg        : (optional) 1/0 to set if genome has genome alignments
  Description: Boolean-style method, returns 1 if genome has genome alignments, 0 if not
  Returntype : 1 or 0
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Boolean Bio::EnsEMBL::MetaData::GenomeInfo::has_other_alignments ( )

  Arg        : (optional) 1/0 to set if genome has other alignments
  Description: Boolean-style method, returns 1 if genome has other alignments, 0 if not
  Returntype : 1 or 0
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Boolean Bio::EnsEMBL::MetaData::GenomeInfo::has_pan_compara ( )

  Arg        : (optional) 1/0 to set if genome is included in pan compara
  Description: Boolean-style method, returns 1 if genome is in pan compara, 0 if not
  Returntype : 1 or 0
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Boolean Bio::EnsEMBL::MetaData::GenomeInfo::has_peptide_compara ( )

  Arg        : (optional) 1/0 to set if genome has peptide compara
  Description: Boolean-style method, returns 1 if genome has peptide, 0 if not
  Returntype : 1 or 0
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Boolean Bio::EnsEMBL::MetaData::GenomeInfo::has_synteny ( )

  Arg        : (optional) 1/0 to set if genome has synteny
  Description: Boolean-style method, returns 1 if genome has synteny, 0 if not
  Returntype : 1 or 0
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo::has_variations ( )

Undocumented method

Code:

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public Bool Bio::EnsEMBL::MetaData::GenomeInfo::is_reference ( )

  Arg        : (optional) value of is_reference
  Description: Gets/sets whether this is a reference for the species
  Returntype : bool
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::name ( )

  Description: Gets unique, compute-safe name for genome
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo::new ( )

Undocumented method

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sub new {
  my ( $class, @args ) = @_;
  my $self = $class->SUPER::new(@args);
  my ( $name,          $display_name, $dbname,
       $species_id,    $taxonomy_id,  $species_taxonomy_id,
       $assembly_name, $assembly_id,  $assembly_level,
       $strain,        $serotype,     $is_reference,
       $organism );
  ( $name,              $display_name,     $dbname,
    $species_id,        $taxonomy_id,      $species_taxonomy_id,
    $assembly_name,     $assembly_id,      $assembly_level,
    $self->{genebuild}, $self->{division}, $strain,
    $serotype,          $is_reference,     $self->{assembly},
    $organism,          $self->{data_release} )
    = rearrange( [ 'NAME',           'DISPLAY_NAME',
                   'DBNAME',         'SPECIES_ID',
                   'TAXONOMY_ID',    'SPECIES_TAXONOMY_ID',
                   'ASSEMBLY_NAME',  'ASSEMBLY_ID',
                   'ASSEMBLY_LEVEL', 'GENEBUILD',
                   'DIVISION',       'STRAIN',
                   'SEROTYPE',       'IS_REFERENCE',
                   'ASSEMBLY',       'ORGANISM',
                   'DATA_RELEASE' ],
                 @args );

  if ( defined $dbname ) {
    $self->add_database( $dbname, $species_id );
  }

  if ( !defined $self->assembly() ) {
    my $ass =
      Bio::EnsEMBL::MetaData::GenomeAssemblyInfo->new(
                                   -ASSEMBLY_NAME       => $assembly_name,
                                   -ASSEMBLY_ID         => $assembly_id,
                                   -ASSEMBLY_LEVEL      => $assembly_level,
                                   -DISPLAY_NAME        => $display_name,
                                   -NAME                => $name,
                                   -STRAIN              => $strain,
                                   -SEROTYPE            => $serotype,
                                   -TAXONOMY_ID         => $taxonomy_id,
                                   -SPECIES_TAXONOMY_ID => $species_taxonomy_id,
                                   -IS_REFERENCE        => $is_reference,
                                   -ORGANISM            => $organism );
    $ass->adaptor( $self->adaptor() ) if defined $self->adaptor();
    $self->assembly($ass);
  }
  return $self;
} ## end sub new

Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public Bio::EnsEMBL::MetaData::GenomeOrganismInfo Bio::EnsEMBL::MetaData::GenomeInfo::organism ( )

  Arg        : (optional) organism object to set
  Description: Gets/sets organism to which genome belongs
  Returntype : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Hashref Bio::EnsEMBL::MetaData::GenomeInfo::other_alignments ( )

  Arg        : (optional) other alignments to set
  Description: Gets/sets other alignments as hashref, keyed by type (dnaAlignFeatures,proteinAlignFeatures)
  			   with values as logic_name-count pairs 
  Returntype : Hashref
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Arrayref Bio::EnsEMBL::MetaData::GenomeInfo::publications ( )

  Description: Gets PubMed IDs for publications associated with the genome
  Returntype : Arrayref of PubMed IDs
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::GenomeInfo::sequences ( )

  Description: Gets array of hashrefs describing sequences from the assembly. Elements are hashrefs with name and acc as keys
  Returntype : Arrayref
  Exceptions : none
  Caller     : general
  Status     : Stable

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public String Bio::EnsEMBL::MetaData::GenomeInfo::serotype ( )

  Description: Gets serotype
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::species_id ( )

  Description: Gets species_id of genome within core database
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::species_taxonomy_id ( )

  Description: Gets NCBI taxonomy ID of species to which this belongs
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::strain ( )

  Description: Gets/sets strain of genome
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::MetaData::GenomeInfo::taxonomy_id ( )

  Description: Gets NCBI taxonomy ID
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Hashref Bio::EnsEMBL::MetaData::GenomeInfo::to_hash ( )

  Description: Render genome as plain hash suitable for export as JSON/XML
  Argument   : (optional) if set to 1, force expansion of children
  Returntype : Hashref
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public String Bio::EnsEMBL::MetaData::GenomeInfo::to_string ( )

  Description: Render genome as string for display
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Arrayref Bio::EnsEMBL::MetaData::GenomeInfo::variations ( )

  Arg        : (optional) variations to set
  Description: Gets/sets variations associated with genomes as hashref 
  			   (variations,structural variations,genotypes,phenotypes), 
  			   further broken down into counts by type/source
  Returntype : Arrayref
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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The documentation for this class was generated from the following file:

Bio/EnsEMBL/MetaData/GenomeInfo.pm

Class Summary

Synopsis

Description

See-also

Available Methods

Method Documentation