EnsEMBL::Web::Object::Variation

Location: /modules/EnsEMBL/Web/Object/Variation.pm
Source code · Permalink

Inherits from:

No subclasses

Overview

Purpose: to store and manipulate ensembl Variation and Variation Feature objects it provides a thin wrapper around the ensembl-core-api

Accessor

Deprecated

Frequencies_table

Individual_genotype_table_calls

Individual_table_calls

Ld

Method

Population_allele_genotype_frequencies

Unknown

  • _availability (EnsEMBL::Web::Object)
  • _filename
  • _help_URL (EnsEMBL::Web::Object)
  • availability
  • availability (EnsEMBL::Web::Object)
  • bp_to_nearest_unit (EnsEMBL::Web::Object)
  • can_export (EnsEMBL::Web::Object)
  • caption
  • consequence_type
  • core_params (EnsEMBL::Web::Object)
  • count_alignments (EnsEMBL::Web::Object)
  • count_ega
  • count_individuals
  • count_populations
  • count_transcripts
  • counts
  • counts (EnsEMBL::Web::Object)
  • fetch_homologues_of_gene_in_species (EnsEMBL::Web::Object)
  • gene_description (EnsEMBL::Web::Object)
  • generate_query_hash
  • generate_query_url (EnsEMBL::Web::Object)
  • getCoordinateSystem (EnsEMBL::Web::Object)
  • get_DASCollection (EnsEMBL::Web::Object)
  • get_adaptor (EnsEMBL::Web::Object)
  • get_external_data
  • get_source
  • location
  • new_image (EnsEMBL::Web::Object)
  • new_karyotype_image (EnsEMBL::Web::Object)
  • new_vimage (EnsEMBL::Web::Object)
  • referer (EnsEMBL::Web::Object)
  • region_name
  • short_caption

Variation_features

Variation_location

Variation_mapping

Variation_object_call

Variation_object_calls

Documentation coverage: 67 %

Methods

    EnsemblObject
    Deprecated. Sets/gets the underlying Ensembl object wrapped by the web object
    Inherited from EnsEMBL::Web::Object
    View source

    Obj
    Accessor. Gets the underlying Ensembl object wrapped by the web object
    Inherited from EnsEMBL::Web::Object
    View source

    URL
    (%params) Returns an absolute link to another script. %params hash is used as the parameters for the link. Note keys species and script are handled differently - as these are not passed as parameters but set the species and script name respectively in the URL
    Inherited from EnsEMBL::Web::Object
    View source

    _URL
    Returns either a full link or absolute link to a script
    Inherited from EnsEMBL::Web::Object
    View source

    _seq_region_
    Variation_location. Args : $unique if $unique=1 -> returns undef if there are more than one variation features returned) if $unique is 0 or undef, it returns the data for the first mapping postion
    Description Gets the sequence region, start and coordinate system name Returns $seq_region, $start, $seq_type
    Example my ($seq_region, $start) = $self->_seq_region_;
    Returns $seq_region, $start, $seq_type
    View source

    add_variation_feature
    Variation_features.
    Args a Bio::EnsEBML::Variation::VariationFeature object Example : $object->add_variation_feature($varfeat);
    Description adds a VariationFeature to the Variation Returns none
    Exceptions thrown if wrong object supplied
    Returns none
    View source

    alleles
    Variation_object_call.
    Args none
    Description gets the SNP alleles Returns Array or string
    Example my $alleles = $object->alleles;
    Returns Array or string
    View source

    alternative_object_from_factory
    There may be occassions when a script needs to work with features of more than one type. in this case we create a new EnsEMBL::Web::Proxy::Factory object for the alternative data type and retrieves the data (based on the standard URL parameters for the new factory) attach it to the universal datahash __data
    Inherited from EnsEMBL::Web::Object
    View source

    ancestor
    Variation_object_calls. Accessor. Example : $object->ancestral_allele;
    Description returns the ancestral allele for the variation Returns String
    Returns String
    View source

    child
    Individual_genotype_table_calls.
    Args Bio::EnsEMBL::Variation::Individual object Example : %children = %{ $object->extra_individual($individual)};
    Description gets any related individuals Returns Bio::EnsEMBL::Variation::Individual
    Returns Bio::EnsEMBL::Variation::Individual
    View source

    command
    Command object attached to proxy object
    Inherited from EnsEMBL::Web::Object
    View source

    dataobj
    Deprecated. Accessor. Gets the underlying Ensembl object wrapped by the web object
    Inherited from EnsEMBL::Web::Object
    View source

    dblinks
    Variation_object_calls.
    Args none
    Description gets the SNPs links to external database Returns Hashref (external DB => listref of external IDs)
    Example my $dblinks = $object->dblinks;
    Returns Hashref (external DB => listref of external IDs)
    View source

    extra_pop
    Frequencies_table.
    Args1 Bio::EnsEMBL::Variation::Population object
    Args2 string "super", "sub" Example : $genotype_freq = $object->extra_pop($pop, "super");
    Description gets any super/sub populations Returns String
    Returns String
    View source

    find_location
    LD.
    Description returns the genomic location for the current slice Returns hash of data
    Example my $data = $object->find_location
    Returns hash of data
    View source

    flanking_seq
    Variation_object_calls. Args: "up" or "down" (string)
    Description gets the sequence downstream of the SNP Returns String
    Example my $down_seq = $object->flanking_seq($down);
    Returns String
    View source

    freqs
    Population_allele_genotype_frequencies.
    Args none
    Description gets allele and genotype frequencies for this Variation Returns hash of data,
    Example my $data = $object->freqs;
    Returns hash of data,
    View source

    freqs_hack
    hacked version of freqs Population_allele_genotype_frequencies.
    Args none
    Description gets allele and genotype frequencies for this Variation Returns hash of data,
    Example my $data = $object->test_freqs;
    Returns hash of data,
    View source

    full_URL
    Returns a full (http://...) link to another script. Wrapper around _URL function
    Inherited from EnsEMBL::Web::Object
    View source

    get_default_pop_name
    LD.
    Description returns population id for default population for this species Returns population dbID
    Example my $pop_id = $object->get_default_pop_name
    Returns population dbID
    View source

    get_genes
    Variation_object_calls. Accessor.
    Args none
    Example my @genes = @ {$obj->get_genes}; Returns arrayref of Bio::EnsEMBL::Gene objects
    Returns arrayref of Bio::EnsEMBL::Gene objects
    View source

    get_individuals_pops
    Individual_genotype_table_calls.

    Args Bio::EnsEMBL::Variation::Individual object Example : $pops = $object->get_individuals_pop($individual)};
    Description gets any individual''s populations Returns Bio::EnsEMBL::Variation::Population
    Returns Bio::EnsEMBL::Variation::Population
    View source

    get_variation_features
    Variation_features.
    Description gets the Variation features found on a variation object; Returns Arrayref of Bio::EnsEMBL::Variation::VariationFeatures
    Example my @vari_features = $object->get_variation_features;
    Returns Arrayref of Bio::EnsEMBL::Variation::VariationFeatures
    View source

    highlights
    Accessor. The highlights array is passed between web-requests to highlight selected items (e.g. Gene around which contigview had been rendered. If any data is passed this is stored in the highlights array and an arrayref of (unique) elements is returned.
    Inherited from EnsEMBL::Web::Object
    View source

    highlights_string
    Returns the highlights area as a | separated list for passing in URLs.
    Inherited from EnsEMBL::Web::Object
    View source

    individual_description
    Individual_genotype_table_calls.
    Args Bio::EnsEMBL::Variation::Individual object Example : $genotype_freq = $object->individual_description($individual);
    Description gets the Individual description Returns String
    Returns String
    View source

    individual_genotype
    Individual_genotype_table_calls.
    Args Bio::EnsEMBL::Variation::IndividualGenotype object Example : $genotype_freq = $object->individual_genotypes($individual);
    Description gets the Individual genotypes Returns String
    Returns String
    View source

    individual_genotypes_obj
    Individual_genotype_table_calls.
    Description gets IndividualGenotypes for this Variation Returns listref of IndividualGenotypes
    Example my $ind_genotypes = $object->individual_genotypes;
    Returns listref of IndividualGenotypes
    View source

    individual_table
    Individual_table_calls.
    Description gets Individual Genotype data for this variation Returns hashref with all the data
    Example my $ind_genotypes = $object->individual_table;
    Returns hashref with all the data
    View source

    interface
    Data interface attached to object
    Inherited from EnsEMBL::Web::Object
    View source

    ld_pops_for_snp
    LD.
    Description gets an LDfeature container for this SNP and calls all the populations on this Returns array ref of population IDs
    Returns array ref of population IDs
    View source

    location_URL
    Parameters: $feature, $script, $contextReturns a link to a contigview style display, based on feature, with context
    Inherited from EnsEMBL::Web::Object
    View source

    location_string
    Variation_location.
    Description Gets chr:start-end for the SNP with 100 bases on either side
    Example my $location = $self->location_string;
    Returns string chr:start-end
    Returns string: chr:start-end
    View source

    mapview_link
    Parameter $feature on a "real chromosome" then this is encapsulated in a link to mapview.Returns name of seq_region $feature is on. If the passed features is
    Inherited from EnsEMBL::Web::Object
    View source

    moltype
    Variation_object_calls. Accessor. Example : $object->moltype;
    Description returns the molecular type of the variation Returns String
    Returns String
    View source

    name
    Variation_object_calls. Accessor.
    Arg (optional)Arg (optional): Variation object name (string)
    Example my $vari_name = $object->vari_name; $object->vari_name('12335'); Returns String for variation name
    Returns String for variation name
    View source

    parent
    Individual_genotype_table_calls. Description=> $self->individual_description($ind_obj),
    Arg2 string "mother" "father" Example : $mother = $object->parent($individual, "mother");
    Args1 Bio::EnsEMBL::Variation::Individual object
    Description gets any related individuals Returns Bio::EnsEMBL::Variation::Individual
    Returns Bio::EnsEMBL::Variation::Individual
    View source

    pop_description
    Frequencies_table.
    Args Bio::EnsEMBL::Variation::Population object Example : $genotype_freq = $object->pop_description($pop);
    Description gets the Population description Returns String
    Returns String
    View source

    pop_genotype_obj
    Frequencies_table.
    Description gets Population genotypes for this Variation Returns listref of Bio::EnsEMBL::Variation::PopulationGenotype
    Example my $pop_genotype_obj = $object->pop_genotype_obj;
    Returns listref of Bio::EnsEMBL::Variation::PopulationGenotype
    View source

    pop_genotypes
    Frequencies_table.
    Args Bio::EnsEMBL::Variation::PopulationGenotype object Example : $genotype_freq = $object->pop_genotypes($pop);
    Description gets the Population genotypes Returns String
    Returns String
    View source

    pop_id
    Frequencies_table.
    Args Bio::EnsEMBL::Variation::Population object Example : $object->pop_id($pop);
    Description gets the Population ID Returns String
    Returns String
    View source

    pop_info
    Frequencies_table.
    Args Bio::EnsEMBL::Variation::Population object
    Description returns a hash with data about this population Returns hash of data
    Example my $data = $self->pop_info
    Returns hash of data
    View source

    pop_links
    Frequencies_table.
    Args Bio::EnsEMBL::Variation::Population object Example : $genotype_freq = $object->pop_links($pop);
    Description gets the Population description Returns String
    Returns String
    View source

    pop_name
    Frequencies_table.
    Args Bio::EnsEMBL::Variation::Population object Example : $object->pop_name($pop);
    Description gets the Population name Returns String
    Returns String
    View source

    pop_obj_from_id
    LD.
    Args Population ID
    Description returns population name for the given population dbID Returns population object
    Example my $pop_name = $object->pop_obj_from_id($pop_id);
    Returns population object
    View source

    pop_size
    Frequencies_table.
    Args Bio::EnsEMBL::Variation::Population object Example : $genotype_freq = $object->pop_size($pop);
    Description gets the Population size Returns String
    Returns String
    View source

    prefix
    Accessor.
    Inherited from EnsEMBL::Web::Object
    View source

    region_type
    Variation_features.
    Args Bio::EnsEMBL::Variation::Variation::Feature
    Description gets the VariationFeature slice seq region name Returns String
    Example my $chr = $data->region_name($vari)
    Returns String
    View source

    seq_region_data
    Variation_location. 'no' if no mapping or 'multiple' if has several hits If there is an error, the first 3 args returned are undef
    Args none
    Description Only returns sequence region, start and coordinate system name if this Variation Object maps to one Variation Feature obj Returns $seq_region, $start, $seq_type, $error(optional) which specifies
    Example my ($seq_region, $start, $type) = $object->seq_region_data;
    Returns $seq_region, $start, $seq_type, $error(optional) which specifies
    View source

    seq_region_end
    Variation_location. Accessor.
    View source

    seq_region_name
    Variation_location. Accessor.
    View source

    seq_region_start
    Variation_location. Accessor.
    View source

    seq_region_strand
    Variation_location. Accessor.
    View source

    seq_region_type
    Variation_location. Accessor.
    View source

    seq_region_type_and_name
    Returns the type/name of seq_region in human readable form - if the coord system type is part of the name this is dropped.
    Inherited from EnsEMBL::Web::Object
    View source

    seq_region_type_human_readable
    Returns the type of seq_region in "human readable form" (in this case just first letter captialised)
    Inherited from EnsEMBL::Web::Object
    View source

    source
    Variation_object_calls.
    Args none
    Description gets the Variation source Returns String
    Example my $vari_source = $object->source;
    Returns String
    View source

    source_version
    Variation_object_calls. Accessor.
    Description gets the Variation source version e.g. dbSNP version 119 Returns String
    Example my $vari_source_version = $object->source
    Returns String
    View source

    start
    Variation_features.
    Args Bio::EnsEMBL::Variation::Variation::Feature
    Description gets the Variation start coordinates Returns String
    Example my $vari_start = $object->start($vari);
    Returns String
    View source

    status
    Variation_object_calls. Accessor.
    Example my $vari_status = $object->get_all_validation_states; Returns List of states
    Returns List of states
    View source

    tagged_snp
    Variation_object_calls.
    Args none
    Description The "is_tagged" call returns an array ref of populations objects Bio::Ensembl::Variation::Population where this SNP is a tag SNP Returns hashref of pop_name
    Example my $pops = $object->tagged_snp
    Returns hashref of pop_name
    View source

    transcript_variation
    Variation_features.

    Args Bio::EnsEMBL::Variation::Variation::Feature
    Description returns SNP consequence (synonymous, stop gained, ...) Returns arrayref of transcript variation objs
    Example my $consequence = $object->consequence($vari);
    Returns arrayref of transcript variation objs
    View source

    unique_variation_feature
    Variation_features.
    Description returns Bio::Ensembl::Variation::Feature object if this Bio::Ensembl::Variation has a unique mapping Returns undef if no mapping
    Returns a arrayref of Bio::Ensembl::Variation::Feature object if multiple mapping
    View source

    var_location
    Variation_location.
    Description Gets chr:start-end for the SNP
    Example my $location = $self->location_string;
    Returns string chr:start-end
    Returns string: chr:start-end
    View source

    vari
    Variation_object_calls.
    Args none
    Description Gets the ensembl variation object stored on the variation data object Returns Bio::EnsEmbl::Variation
    Example my $ensembl_vari = $object->vari
    Returns Bio::EnsEmbl::Variation
    View source

    vari_class
    Variation_object_calls. Accessor.
    Description returns the variation class (indel, snp, het) for a varation Returns String
    Example my $vari_class = $object->vari_class
    Returns String
    View source

    variation_feature_mapping
    Variation_mapping.
    Description gets the Variation features found on a variation object; Returns Arrayref of Bio::EnsEMBL::Variation::VariationFeatures
    Example my @vari_features = $object->variation_feature_mappin
    Returns Arrayref of Bio::EnsEMBL::Variation::VariationFeatures
    View source