Bio::EnsEMBL::Variation::DBSQL::DBAdaptor Class Reference

Inheritance diagram for Bio::EnsEMBL::Variation::DBSQL::DBAdaptor:

List of all members.

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Class Summary

Synopsis

Description

This module provides a connection to an Ensembl variation database and
provides a means to obtain ObjectAdaptors.

Definition at line 20 of file DBAdaptor.pm.

Available Methods
protected Bio::EnsEMBL::ExternalFeatureFactory	_each_DASFeatureFactory ()
protected	_exclude_failed_alleles_constraint ()
protected	_exclude_failed_constraint ()
protected	_exclude_failed_structural_variations_constraint ()
protected	_exclude_failed_variations_constraint ()
protected	_get_schema_build ()
public void	add_DASFeatureFactory ()
public void	add_db_adaptor ()
public void	add_ExternalFeatureAdaptor ()
public void	add_ExternalFeatureFactory ()
public void	add_GenericFeatureAdaptor ()
public Array	all_species ()
public	AUTOLOAD ()
public void	clear_caches ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public	DESTROY ()
public Dna	dnadb ()
public void	find_and_add_aliases ()
public void	find_and_add_species_id ()
public Adaptor	get_adaptor ()
public Hash	get_all_db_adaptors ()
public	get_available_adaptors ()
public Bio::EnsEMBL::DBSQL::DBConnection	get_db_adaptor ()
public Reference	get_ExternalFeatureAdaptors ()
public Reference	get_GenericFeatureAdaptors ()
public Bio::EnsEMBL::Utils::SeqRegionCache	get_SeqRegionCache ()
public String	group ()
public Boolean	has_switched_adaptor ()
public Int	include_failed_variations ()
public Int	include_non_significant_phenotype_associations ()
public Boolean	is_multispecies ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	new ()
public Int	no_cache ()
public	remove_all_DASFeatureFactories ()
public void	remove_db_adaptor ()
public The	revert_adaptor ()
public void	set_adaptor ()
public Int	shift_hgvs_variants_3prime ()
public String	species ()
public String	species_id ()
public void	switch_adaptor ()
public Hash	to_hash ()
public Int	use_vcf ()
public	vcf_config ()
public	vcf_config_file ()
public	vcf_root_dir ()
public	vcf_tmp_dir ()

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Method Documentation

protected Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::_exclude_failed_alleles_constraint

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Undocumented method

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protected Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::_exclude_failed_constraint

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Undocumented method

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protected Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::_exclude_failed_structural_variations_constraint

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Undocumented method

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protected Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::_exclude_failed_variations_constraint

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Undocumented method

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public Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::get_available_adaptors

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Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::DBSQL::DBAdaptor.

public Int Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::include_failed_variations

(

)

  Arg [1]    : int $newval (optional)
  Example    :

        #Get a DBAdaptor for the human variation database
        my $dba = $registry->get_DBAdaptor('human','variation');
        
        #Configure the DBAdaptor to return failed variations when using
        #fetch methods in the various object adaptors
        $dba->include_failed_variations(1);
        
        #Get a variation set adaptor
        my $vs_adaptor = $dba->get_VariationSetAdaptor();
        
        #Get a variation set for the 1000 genomes high coverage Yoruba trio data
        my $vs = $vs_adaptor->fetch_by_name('1000 genomes - High coverage - Trios - YRI');
        
        # Get the iterator for the variations belonging to this variation set.
        #This will now include variations that has been flagged as being failed.
        #The default behaviour is not to return these.
        my $it = $vs->get_Variation_Iterator();
        
        # Iterate over the variations
        while ($it->has_next()) {
        
            # Get the next variation object in the iterator
            my $v = $it->next();
            
            # Check if the variation is flagged as failed
            if ($v->is_failed()) {
            # Do something...
            }
            # If not, check if any of its subsnps have been flagged as failed
            elsif ($v->has_failed_alleles()) {
            #Do something else...
            }
            else {
            #Do something else...
            }
        }

  Description: Getter/Setter for the behaviour of the adaptors connected through this
	       DBAdaptor when it comes to variations and alleles that have been flagged as failed.
	       The default behaviour is not to return these variations or alleles in e.g. the
	       'fetch_all_by...'-type methods. If this flag is set, those methods will
	       instead also return failed variations and alleles. Note that a variation is considered
	       failed when the variation itself is failed. If only some alleles belonging
	       to the variation are failed, the entire variation will not be considered
	       to be failed.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

public Int Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::include_non_significant_phenotype_associations

(

)

  Arg [1]    : int $newval (optional)
  Example    :

    # Get a DBAdaptor for the human variation database
    my $dba = $registry->get_DBAdaptor('human','phenotypefeature');
    
    # Configure the DBAdaptor to return non significant phenotype associations when using
    # fetch methods in the various object adaptors
    $dba->include_non_significant_phenotype_associations(1);

  Description: Getter/Setter for the behaviour of the adaptors connected through this
         DBAdaptor when it comes to phenotype feature.
         The default behaviour is to return the phenotype features with significance results only e.g. the
         'fetch_all_by...'-type methods. If this flag is set, those methods will
         instead also return phenotype features with non significant results. 
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

public Int Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::shift_hgvs_variants_3prime

(

)

  Arg [1]    : int $newval (optional)
  Example    :

        #Get a DBAdaptor for the human variation database
        my $dba = $registry->get_DBAdaptor('human','variation');
        
        #Configure the DBAdaptor to return failed variations when using
        #fetch methods in the various object adaptors
        $dba->shift_hgvs_variants_3prime(1);
        
        #Proceed to extract HGVS annotation as normal

  Description: Getter/Setter for the behaviour of the adaptors connected through this
	       DBAdaptor when it comes to HGVS transcript and protein level annotation.
	       The default behaviour is to keep the positions as input. Formal HGVS annotation
               requires any variant to be described at the most 3 prime location possible which 
               changes the variation consequence in a very small number of cases.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : at risk

Code:

public Int Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::use_vcf

(

)

  Arg [1]    : int $newval (optional)
  Example    :

        # Get a LD feature container adaptor
        my $ldfca = $registry->get_DBAdaptor('human','variation','ldfeaturecontainer');
        
        # tell the adaptor to include genotypes from VCF files
        $ldfca->db->use_vcf(1);
        
        # fetch LD container as normal
    my $ldfc = $ldfca->fetch_by_Slice($slice, $population);

  Description: Getter/Setter the use_vcf property. Switching this to a
               non-zero value instructs the API to look in configured
               VCF files for genotype-based data. Setting to 1 tells the
               API to use both the DB and VCF; setting to 2 tells the API
               to use only VCF.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : at risk

Code:

public Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::vcf_config

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Undocumented method

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public Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::vcf_config_file

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Undocumented method

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public Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::vcf_root_dir

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Undocumented method

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public Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::vcf_tmp_dir

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Undocumented method

Code:

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

• Variation/DBSQL/DBAdaptor.pm