module EnsemblREST::VEP

Public Instance Methods

hgvs_get(hgvs_notation, species = 'human', options = {}) click to toggle source

Fetch variant consequences based on a HGVS notation

@param [String] hgvs_notation HGVS notation. May be genomic (g), coding © or protein (p), with reference to chromosome name, gene name, transcript ID or protein ID. @param [String] species Species name/alias @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/vep_hgvs_get @return [JSON] Variants consequences

# File lib/ensemblrest/vep.rb, line 45
def hgvs_get(hgvs_notation, species = 'human', options = {})
        return EnsemblREST.get("vep/#{species}/hgvs/#{hgvs_notation}", {format: 'json'}.merge(options))
end
id_get(id, species = 'human', options = {}) click to toggle source

Fetch variant consequences based on a variation identifier

@param [String] id Query ID. Supports dbSNP, COSMIC and HGMD identifiers @param [String] species Species name/alias @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/vep_region_get @return [JSON] Variants consequences

# File lib/ensemblrest/vep.rb, line 35
def id_get(id, species = 'human', options = {})
        return EnsemblREST.get("vep/#{species}/id/#{id}", {format: 'json'}.merge(options))
end
id_post(ids, species = 'human', options = {}) click to toggle source

Fetch variant consequences for multiple ids

@param [Array] ids Query IDs. Supports dbSNP, COSMIC and HGMD identifiers @param [String] species Species name/alias @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/vep_id_post @return [JSON] Variants consequences

# File lib/ensemblrest/vep.rb, line 55
def id_post(ids, species = 'human', options = {})
        return EnsemblREST.post("vep/#{species}/id", {"ids" => ids}, {format: 'json'}.merge(options))
end
region_get(allele, region, species = 'human', options = {}) click to toggle source

Fetch variant consequences

@param [String] allele Variation allele, Example Values: ‘C’, ‘DUP’ @param [String] region Query region. Example Values: ‘9:22125503-22125502:1’, ‘7:100318423-100321323:1’ @param [String] species Species name/alias @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/vep_region_get @return [JSON] Variants consequences

# File lib/ensemblrest/vep.rb, line 25
def region_get(allele, region, species = 'human', options = {})
        return EnsemblREST.get("vep/#{species}/region/#{region}/#{allele}", {format: 'json'}.merge(options))
end
region_post(variants, species = 'human', options = {}) click to toggle source

Fetch variant consequences for multiple regions

@param [Array] variants input lines for VEP. Example Values: [“21 26960070 rs116645811 G A . . .”, “21 26965148 rs1135638 G A . . .” ] @param [String] species Species name/alias @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/vep_region_get @return [JSON] Variants consequences

# File lib/ensemblrest/vep.rb, line 65
def region_post(variants, species = 'human', options = {})
        return EnsemblREST.post("vep/#{species}/region", {"variants" => variants}, {format: 'json'}.merge(options))
end