module Exodb::Ensembl::REST
Public Instance Methods
assembly_map(region, asm_two, asm_one = Exodb::DEFAULTASSEMBLY, species = 'human', options = {})
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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)
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# 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 = {})
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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 = {})
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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 = {})
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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