module Exodb::Ensembl::REST

Public Instance Methods

assembly_map(region, asm_two, asm_one = Exodb::DEFAULTASSEMBLY, species = 'human', options = {}) click to toggle source

Converse coordinate from one asembly to another from rest.ensembl.org/documentation/info/assembly_map

@param [String] location string in chromosome:start..stop format @param [String] target assembly or asm_two @param [String] original assembly default: exodb::DEFAULTASSEMBLY @param [String] species of genome @param [Hash] option

# File lib/exodb/utils/ensemblrest.rb, line 51
def assembly_map(region, asm_two, asm_one = Exodb::DEFAULTASSEMBLY, species = 'human', options = {})
        return Exodb::Ensembl::REST.get("map/#{species.gsub(/\s+/, '_')}/#{Exodb::ASSEMBLY[asm_one.downcase]}/#{region}/#{Exodb::ASSEMBLY[asm_two.downcase]}", options)
end
get(get_path, options) click to toggle source
# File lib/exodb/utils/ensemblrest.rb, line 22
def get(get_path, options)
        request = Net::HTTP::Get.new(get_path, {'Content-Type' => 'application/json'}.merge(options))
        response = @@http.request(request)
        if response.code != "200"
                riase InvalidResponse, "Invalid response: #{response.code}"
        else
                return JSON.parse(response.body)
        end
end
sequence_region(region, species, options = {}) click to toggle source

Returns the genomic sequence of the specified region of the given species. from rest.ensembl.org/documentation/info/sequence_region

@param [String] location string in chromosome:start..stop format @param [String] species of genome @param [Fasta] Return sequence

# File lib/exodb/utils/ensemblrest.rb, line 61
def sequence_region(region, species, options = {})
        return Exodb::Ensembl::REST.get("sequence/region/#{species}/#{region}", {'Content-Type' => 'text/x-fasta', 'coord_system_version' => Exodb::DEFAULTASSEMBLY}.merge(options))
end
vep_hgvs_get(hgvs, species, options = {}) click to toggle source

rest.ensembl.org/documentation/info/vep_hgvs_get

# File lib/exodb/utils/ensemblrest.rb, line 39
def vep_hgvs_get(hgvs, species, options = {})
        return Exodb::Ensembl::REST.get("vep/#{species}/hgvs/#{region}/allele", options)
end
vep_region_get(region, allele, species, options = {}) click to toggle source

rest.ensembl.org/documentation/info/vep_region_get

# File lib/exodb/utils/ensemblrest.rb, line 34
def vep_region_get(region, allele, species, options = {})
        return Exodb::Ensembl::REST.get("vep/#{species}/region/#{region}/allele", options)
end