EnsEMBL::Web::Object::Variation

Methods

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


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


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
EnsEMBL::Web::Object::URL


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


_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
EnsEMBL::Web::Object::Variation::_seq_region_


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
EnsEMBL::Web::Object::Variation::add_variation_feature


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
EnsEMBL::Web::Object::Variation::alleles


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
EnsEMBL::Web::Object::alternative_object_from_factory


ancestor
Variation_object_calls. Accessor. Example : $object->ancestral_allele;

Description

returns the ancestral allele for the variation Returns String

Returns String
View source
EnsEMBL::Web::Object::Variation::ancestor


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
EnsEMBL::Web::Object::Variation::child


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


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


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
EnsEMBL::Web::Object::Variation::dblinks


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
EnsEMBL::Web::Object::Variation::extra_pop


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
EnsEMBL::Web::Object::Variation::find_location


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
EnsEMBL::Web::Object::Variation::flanking_seq


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
EnsEMBL::Web::Object::Variation::freqs


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
EnsEMBL::Web::Object::Variation::freqs_hack


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


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
EnsEMBL::Web::Object::Variation::get_default_pop_name


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
EnsEMBL::Web::Object::Variation::get_genes


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
EnsEMBL::Web::Object::Variation::get_individuals_pops


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
EnsEMBL::Web::Object::Variation::get_variation_features


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
EnsEMBL::Web::Object::highlights


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


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
EnsEMBL::Web::Object::Variation::individual_description


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
EnsEMBL::Web::Object::Variation::individual_genotype


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
EnsEMBL::Web::Object::Variation::individual_genotypes_obj


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
EnsEMBL::Web::Object::Variation::individual_table


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


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
EnsEMBL::Web::Object::Variation::ld_pops_for_snp


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
EnsEMBL::Web::Object::location_URL


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
EnsEMBL::Web::Object::Variation::location_string


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
EnsEMBL::Web::Object::mapview_link


moltype
Variation_object_calls. Accessor. Example : $object->moltype;

Description

returns the molecular type of the variation Returns String

Returns String
View source
EnsEMBL::Web::Object::Variation::moltype


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
EnsEMBL::Web::Object::Variation::name


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
EnsEMBL::Web::Object::Variation::parent


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
EnsEMBL::Web::Object::Variation::pop_description


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
EnsEMBL::Web::Object::Variation::pop_genotype_obj


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
EnsEMBL::Web::Object::Variation::pop_genotypes


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
EnsEMBL::Web::Object::Variation::pop_id


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
EnsEMBL::Web::Object::Variation::pop_info


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
EnsEMBL::Web::Object::Variation::pop_links


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
EnsEMBL::Web::Object::Variation::pop_name


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
EnsEMBL::Web::Object::Variation::pop_obj_from_id


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
EnsEMBL::Web::Object::Variation::pop_size


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


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
EnsEMBL::Web::Object::Variation::region_type


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
EnsEMBL::Web::Object::Variation::seq_region_data


seq_region_end
Variation_location. Accessor.
View source
EnsEMBL::Web::Object::Variation::seq_region_end


seq_region_name
Variation_location. Accessor.
View source
EnsEMBL::Web::Object::Variation::seq_region_name


seq_region_start
Variation_location. Accessor.
View source
EnsEMBL::Web::Object::Variation::seq_region_start


seq_region_strand
Variation_location. Accessor.
View source
EnsEMBL::Web::Object::Variation::seq_region_strand


seq_region_type
Variation_location. Accessor.
View source
EnsEMBL::Web::Object::Variation::seq_region_type


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
EnsEMBL::Web::Object::seq_region_type_and_name


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
EnsEMBL::Web::Object::seq_region_type_human_readable


source
Variation_object_calls.

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

Returns String
View source
EnsEMBL::Web::Object::Variation::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
EnsEMBL::Web::Object::Variation::source_version


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
EnsEMBL::Web::Object::Variation::start


status
Variation_object_calls. Accessor.

Example

my $vari_status = $object->get_all_validation_states; Returns List of states

Returns List of states
View source
EnsEMBL::Web::Object::Variation::status


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
EnsEMBL::Web::Object::Variation::tagged_snp


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
EnsEMBL::Web::Object::Variation::transcript_variation


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
EnsEMBL::Web::Object::Variation::unique_variation_feature


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
EnsEMBL::Web::Object::Variation::var_location


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
EnsEMBL::Web::Object::Variation::vari


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
EnsEMBL::Web::Object::Variation::vari_class


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
EnsEMBL::Web::Object::Variation::variation_feature_mapping