Ensembl Genomes API
Auxillary Perl API for Ensembl Genomes
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Bio::EnsEMBL::Utils::MetaData::GenomeInfo Class Reference

Public Member Functions

public new ()
 
public species ()
 
public String strain ()
 
public String serotype ()
 
public String name ()
 
public String dbname ()
 
public String species_id ()
 
public String taxonomy_id ()
 
public String assembly_name ()
 
public String assembly_id ()
 
public String assembly_level ()
 
public String genebuild ()
 
public String division ()
 
public String db_size ()
 
public base_count ()
 
public Arrayref aliases ()
 
public Arrayref compara ()
 
public Arrayref sequences ()
 
public Arrayref publications ()
 
public Arrayref variations ()
 
public Hashref features ()
 
public Hashref annotations ()
 
public Hashref other_alignments ()
 
public has_variations ()
 
public Boolean has_genome_alignments ()
 
public Boolean has_synteny ()
 
public Boolean has_peptide_compara ()
 
public Boolean has_pan_compara ()
 
public Boolean has_other_alignments ()
 
public Int count_variation ()
 
public Int count_alignments ()
 
public Uniprot get_uniprot_coverage ()
 
public Hashref to_hash ()
 
public count_hash_values ()
 
public Int count_hash_lengths ()
 
public DbID dbID ()
 
public
Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor 		adaptor ()
 
protected void _preload ()
 
protected _unload ()
 

Detailed Description

Synopsis

my $genome = Bio::EnsEMBL::Utils::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";

Member Function Documentation

protected void Bio::EnsEMBL::Utils::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

/**

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

Undocumented method

Code:
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public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor Bio::EnsEMBL::Utils::MetaData::GenomeInfo::adaptor ( ) 
  Arg        : (optional) adaptor to set set
  Description: Gets/sets GenomeInfoAdaptor
  Returntype : Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor
  Exceptions : none
  Caller     : Internal
  Status     : Stable
Code:
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public Arrayref Bio::EnsEMBL::Utils::MetaData::GenomeInfo::aliases ( ) 
  Arg        : (optional) arrayref of aliases to set
  Description: Gets/sets 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::Utils::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 String Bio::EnsEMBL::Utils::MetaData::GenomeInfo::assembly_id ( ) 
  Arg        : (optional) assembly_id to set
  Description: Gets/sets INSDC accession for assembly
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::Utils::MetaData::GenomeInfo::assembly_level ( ) 
  Arg        : (optional) assembly_level to set
  Description: Gets/sets highest level of assembly (chromosome, supercontig etc.)
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::Utils::MetaData::GenomeInfo::assembly_name ( ) 
  Arg        : (optional) assembly_name to set
  Description: Gets/sets name of assembly
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo::base_count ( )

Undocumented method

Code:
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public Arrayref Bio::EnsEMBL::Utils::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::Utils::MetaData::GenomeComparaInfo
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Int Bio::EnsEMBL::Utils::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::Utils::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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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo::count_hash_values ( )

Undocumented method

Code:
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public Int Bio::EnsEMBL::Utils::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 String Bio::EnsEMBL::Utils::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::Utils::MetaData::GenomeInfo::dbID ( ) 
  Arg        : (optional) base_count to set
  Description: Gets/sets total number of bases in assembled genome
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

/**

  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::Utils::MetaData::DBSQL::GenomeInfoAdaptor
  Status     : Stable
Code:
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public String Bio::EnsEMBL::Utils::MetaData::GenomeInfo::dbname ( ) 
  Arg        : (optional) dbname to set
  Description: Gets/sets name of core database from which genome comes
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::Utils::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::Utils::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::Utils::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::Utils::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::Utils::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::Utils::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::Utils::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::Utils::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
Code:
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public Boolean Bio::EnsEMBL::Utils::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
Code:
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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo::has_variations ( )

Undocumented method

Code:
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public String Bio::EnsEMBL::Utils::MetaData::GenomeInfo::name ( ) 
  Arg        : (optional) name to set
  Description: Gets/sets readable display name for genome
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo::new ( )

Undocumented method

Code:
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public Hashref Bio::EnsEMBL::Utils::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::Utils::MetaData::GenomeInfo::publications ( ) 
  Arg        : (optional) arrayref of pubmed IDs to set
  Description: Gets/sets PubMed IDs for publications associated with the genome
  Returntype : Arrayref of PubMed IDs
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Arrayref Bio::EnsEMBL::Utils::MetaData::GenomeInfo::sequences ( ) 
  Arg        : (optional) arrayref of sequences to set
  Description: Gets/sets 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
Code:
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public String Bio::EnsEMBL::Utils::MetaData::GenomeInfo::serotype ( ) 
  Arg        : (optional) serotype to set
  Description: Gets/sets serotype
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo::species ( )

Undocumented method

Code:
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public String Bio::EnsEMBL::Utils::MetaData::GenomeInfo::species_id ( ) 
  Arg        : (optional) species_id to set
  Description: Gets/sets species_id of genome within core database
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::Utils::MetaData::GenomeInfo::strain ( ) 
  Arg        : (optional) strain to set
  Description: Gets/sets strain of genome
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::Utils::MetaData::GenomeInfo::taxonomy_id ( ) 
  Arg        : (optional) taxonomy_id to set
  Description: Gets/sets NCBI taxonomy ID
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Hashref Bio::EnsEMBL::Utils::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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public Arrayref Bio::EnsEMBL::Utils::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:
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