module EnsemblREST::Comparative
Public Instance Methods
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
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
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
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
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
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