module EnsemblREST::Comparative

Public Instance Methods

genetree(id, options = {}) click to toggle source

Retrieves a gene tree dump for a gene tree stable identifier

@param [String] id An Ensembl genetree ID @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/genetree @return [JSON] a gene tree

# File lib/ensemblrest/comparativegenomics.rb, line 23
def genetree(id, options = {})
        return EnsemblREST.get("genetree/id/#{id}", {format: 'json'}.merge(options))
end
genetree_member_id(id, options = {}) click to toggle source

Retrieves a gene tree that contains the stable identifier

@param [String] id An Ensembl stable ID @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/genetree_member_id @return [JSON] gene trees

# File lib/ensemblrest/comparativegenomics.rb, line 32
def genetree_member_id(id, options = {})
        return EnsemblREST.get("genetree/member/id/#{id}", {format: 'json'}.merge(options))
end
genetree_member_symbol(symbol, species = 'human', options = {}) click to toggle source

Retrieves a gene tree containing the gene identified by a symbol

@param [String] symbol Symbol or display name of a gene @param [String] species Species name/alias @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/genetree_member_symbol @return [JSON] gene trees

# File lib/ensemblrest/comparativegenomics.rb, line 42
def genetree_member_symbol(symbol, species = 'human', options = {})
        return EnsemblREST.get("genetree/member/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
end
genomic_alignment_region(region, species = 'human', options = {}) click to toggle source

Retrieves genomic alignments as separate blocks based on a region and species

@param [String] region Query region. A maximum of 10Mb is allowed to be requested at any one time @param [String] species Species name/alias @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/genomic_alignment_region @return [JSON] an alignment

# File lib/ensemblrest/comparativegenomics.rb, line 52
def genomic_alignment_region(region, species = 'human', options = {})
        return EnsemblREST.get("alignment/region/#{species}/#{region}", {format: 'json'}.merge(options))
end
homology_ensemblgene(id, options = {}) click to toggle source

Retrieves homology information (orthologs) by Ensembl gene id

@param [String] id An Ensembl stable ID @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/homology_ensemblgene @return [JSON] a homology information

# File lib/ensemblrest/comparativegenomics.rb, line 61
def homology_ensemblgene(id, options = {})
        return EnsemblREST.get("homology/id/#{id}", {format: 'json'}.merge(options))
end
homology_symbol(symbol, species = 'human', options = {}) click to toggle source

Retrieves homology information (orthologs) by symbol

@param [String] symbol Symbol or display name of a gene @param [String] species Species name/alias @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/homology_symbol @return [JSON] gene trees

# File lib/ensemblrest/comparativegenomics.rb, line 71
def homology_symbol(symbol, species = 'human', options = {})
        return EnsemblREST.get("homology/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
end