ensemblrest 0.0.5 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a85972ee3e540b01b703eabba40b18b86a0c9846
-  data.tar.gz: 6b5317110ad84500394cf550835271ed6d6a7fd3
+  metadata.gz: 61c74f74f07aaedc9f7f77b799d7965ab583f306
+  data.tar.gz: 4138d77a8d0fe8c1ee791500c55fca7b6b0d0b15
 SHA512:
-  metadata.gz: bf53774dad64eb9032f1a75f56ffe0ff98c4c4e1fa3100d868d008e0b9e0eb08df99b346b6cebfdab8477b06a69551b2f13850854c21ec9d5a2de8c7fc6a645e
-  data.tar.gz: 6409a4555e6acdf7ae5a455a37f54585f761a78d37abba9bd98426b7454d62431a183f7060a8512e05c6aaa47cad726661fecb6a338349d7419692a51e936633
+  metadata.gz: 98a42e9f686cce15bb8d0c376957df4420d2e75620bfdf29fa1d165671a9743ea0b28960f1bac049d1863d4d34d664eb037df7b6bcc6a658385f8d1749a0ff74
+  data.tar.gz: d62c2fc1e5b6feaa29a553a4b7e976d6e26588c90c70e49373e047acfa0ed5c95d78e80186991e613e732c0f574d199464c2d888926d66acfeae27329277a31b

data/lib/ensemblrest.rb

@@ -20,19 +20,18 @@ require 'json'
 require 'csv'
 require 'digest'
 
+require 'ensemblrest/version'
 require 'ensemblrest/connect'
 require 'ensemblrest/sequence'
 require 'ensemblrest/map'
-require 'ensemblrest/version'
-
-#p EnsemblREST::sequence_id("ENSP00000288602")
-#p EnsemblREST::sequence_region("X:1000000..1000100:1", 'human')
-#
-#p EnsemblREST::assembly_cdna("ENST00000288602", "100..300")
-#p EnsemblREST::assembly_cds('ENST00000288602', '1..1000')
-#p EnsemblREST::assembly_map('human', 'GRCh37' , 'X:1000000..1000100:1', 'GRCh38')
-#p EnsemblREST::assembly_translation('ENSP00000288602', '100..300')
-#EnsemblREST.use37
-#
-#p EnsemblREST::sequence_id('ENST00000288602', type: 'cdna').seq.length
-#p EnsemblREST::sequence_id('ENST00000288602', type: 'cds').seq.length
+require 'ensemblrest/vep'
+require 'ensemblrest/overlap'
+require 'ensemblrest/archive'
+require 'ensemblrest/comparativegenomics'
+require 'ensemblrest/xref'
+require 'ensemblrest/info'
+require 'ensemblrest/lookup'
+require 'ensemblrest/ontoandtaxo'
+require 'ensemblrest/regulation'
+require 'ensemblrest/variation'
+require 'ensemblrest/variationga4gh'

data/lib/ensemblrest/archive.rb

@@ -0,0 +1,34 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+	
+	module Archive
+		module_function
+		# Uses the given identifier to return the archived sequence
+		# 
+		# @param [String] An Ensembl stable ID
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_get
+		# @return [JSON] Variants consequences
+		def id_get(id, options = {})
+			return EnsemblREST.get("archive/id/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Retrieve the archived sequence for a set of identifiers
+		# 
+		# @param [Array] Ensembl stable IDs
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_post
+		# @return [JSON] Requested response
+		def id_post(ids, options = {})
+			return EnsemblREST.post("archive/id", {"id" => ids}, {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/comparativegenomics.rb

@@ -0,0 +1,75 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+
+	module Comparative
+	
+		module_function
+		
+		# Retrieves a gene tree dump for a gene tree stable identifier
+		# 
+		# @param [String] An Ensembl genetree ID
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree
+		# @return [JSON] a gene tree
+		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] An Ensembl stable ID
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_id
+		# @return [JSON] gene trees
+		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 or display name of a gene
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_symbol
+		# @return [JSON] gene trees
+		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] Query region. A maximum of 10Mb is allowed to be requested at any one time
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genomic_alignment_region
+		# @return [JSON] an alignment
+		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] An Ensembl stable ID
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_ensemblgene
+		# @return [JSON] a homology information
+		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 or display name of a gene
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_symbol
+		# @return [JSON] gene trees
+		def homology_symbol(symbol, species = 'human', options = {})
+			return EnsemblREST.get("homology/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/connect.rb

@@ -1,6 +1,6 @@
-# 
 # Bio-ensemblrest
-# Copyright (C) 2014
+# 
+# Copyright (C) 2015
 #
 # author: Natapol Pornputtapong <natapol.por@gmail.com>
 #
@@ -27,33 +27,48 @@ module EnsemblREST
 		'xml' => 'text/xml',
 		'yaml' => 'text/x-yaml'
 	}
+	
+	class InvalidResponse < Exception
+		
+	end
+	
+	class ServiceNotFound < Exception
 		
+	end
 	
 	module_function
 	
+	# Connect to Ensembl REST Service
+	# 
+	# @param [String] Base Ensembl REST Service URL
 	def connect(server)
 		@@url = URI.parse(server)
 		@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
 	end
 	
+	# Switch to use GRCh37 assembly version
 	def use_GRCh37
 		@@url = URI.parse('http://grch37.rest.ensembl.org/')
 		@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
 	end
 	
+	# Switch to use GRCh37 assembly version
 	def use37
 		EnsemblREST::use_GRCh37
 	end
 	
+	# Switch to use GRCh38 assembly version
 	def use_GRCh38
 		@@url = URI.parse('http://rest.ensembl.org/')
 		@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
 	end
 	
+	# Switch to use GRCh38 assembly version
 	def use38
 		EnsemblREST::use_GRCh38
 	end
 	
+	# Parse options use in the Module only
 	def parse_options(options)
 		parsed_options = {opts: [], format: {}}
 		options.each do |k, v|
@@ -62,13 +77,14 @@ module EnsemblREST
 			elsif k.to_s == 'content-type'
 				parsed_options[:format] = {'content-type' => v}
 			else
-				parsed_options[:opts].push case v.class
-				when TrueClass
-					"#{k}=1"
-				when FalseClass
-					"#{k}=0"
+				if v.is_a?(TrueClass)
+					parsed_options[:opts].push("#{k}=1")
+				elsif v.is_a?(FalseClass)
+					parsed_options[:opts].push("#{k}=0")
+				elsif v.is_a?(Array)
+					v.each {|member| parsed_options[:opts].push("#{k}=#{member}")}
 				else
-					"#{k}=#{v}"
+					parsed_options[:opts].push("#{k}=#{v}")
 				end
 			end
 			
@@ -76,6 +92,7 @@ module EnsemblREST
 		return parsed_options
 	end
 	
+	# Parse responses use in the Module only
 	def parse_response(response, type)
 		case response.code
 		when '200'
@@ -91,19 +108,25 @@ module EnsemblREST
 			else
 				return response.body
 			end
+		when '404'
+			raise EnsemblREST::ServiceNotFound, "Service not found"
 		else
-			raise "Invalid response: #{response.code}"
+			raise EnsemblREST::InvalidResponse, "Invalid response: #{response.code}"
 		end
 	end
 	
+	# Do a get request
 	def get(get_path, options)
 		parsed_options = EnsemblREST::parse_options(options)
 		request = Net::HTTP::Get.new("#{get_path}#{parsed_options[:opts].empty? ? '' : "?#{parsed_options[:opts].join(';')}"}", parsed_options[:format])
 		return EnsemblREST::parse_response(@@http_connect.request(request), parsed_options[:format]['content-type'])
 	end
 	
-	#def post(get_path, request_body, options)
-	#	request = Net::HTTP::Get.new(get_path, EnsemblREST::parse_format(options))
-	#	return EnsemblREST::parse_response(@@http_connect.request(request), options['Content-Type'])
-	#end
+	# Do a post request
+	def post(post_path, request_body, options)
+		parsed_options = EnsemblREST::parse_options(options)
+		request = Net::HTTP::Post.new(post_path, parsed_options[:format].merge({'Accept' => 'application/json'}))
+		request.body = request_body.to_json
+		return EnsemblREST::parse_response(@@http_connect.request(request), parsed_options[:format]['content-type'])
+	end
 end

data/lib/ensemblrest/info.rb

@@ -0,0 +1,134 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+	
+	module Info
+		module_function
+		
+		# List the names of analyses involved in generating Ensembl data.
+		# 
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/analysis
+		# @return [JSON] List the names of analyses
+		def analysis(species = 'human', options = {})
+			return EnsemblREST.get("info/analysis/#{species}", {format: 'json'}.merge(options))
+		end
+		
+		# List the currently available assemblies for a species.
+		# 
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_info
+		# @return [JSON] List the currently available assemblies
+		def assembly_info(species = 'human', options = {})
+			return EnsemblREST.get("info/assembly/#{species}", {format: 'json'}.merge(options))
+		end
+		
+		# Returns information about the specified toplevel sequence region for the given species.
+		# 
+		# @param [String] The (top level) sequence region name.
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_stats
+		# @return [JSON] Returns information about the specified toplevel sequence region
+		def assembly_stats(region_name, species = 'human', options = {})
+			return EnsemblREST.get("info/assembly/#{species}/#{region_name}", {format: 'json'}.merge(options))
+		end
+		
+		# List the functional classifications of gene models that Ensembl associates with a particular species. 
+		# Useful for restricting the type of genes/transcripts retrieved by other endpoints.
+		# 
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/biotypes
+		# @return [JSON] List the currently available assemblies
+		def biotypes(species = 'human', options = {})
+			return EnsemblREST.get("info/biotypes/#{species}", {format: 'json'}.merge(options))
+		end
+		
+		# List all compara analyses available (an analysis defines the type of comparative data).
+		# 
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_methods
+		# @return [JSON] List all compara analyses
+		def compara_methods(options = {})
+			return EnsemblREST.get("info/compara/methods", {format: 'json'}.merge(options))
+		end
+		
+		# List all collections of species analysed with the specified compara method.
+		# 
+		# @param [String] Filter by compara method. Use one the methods returned by /info/compara/methods endpoint.
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_species_sets
+		# @return [JSON] List the currently available assemblies
+		def compara_species_sets(method, options = {})
+			return EnsemblREST.get("info/compara/species_sets/#{method}", {format: 'json'}.merge(options))
+		end
+		
+		# Lists all available comparative genomics databases and their data release.
+		# 
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/comparas
+		# @return [JSON] List all compara analyses
+		def comparas(options = {})
+			return EnsemblREST.get("info/comparas", {format: 'json'}.merge(options))
+		end
+		
+		# Shows the data releases available on this REST server. May return more than one release (unfrequent non-standard Ensembl configuration).
+		# 
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/data
+		# @return [JSON] Shows the data releases available on this REST server
+		def data(options = {})
+			return EnsemblREST.get("info/data", {format: 'json'}.merge(options))
+		end
+		
+		# Lists all available external sources for a species.
+		# 
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/external_dbs
+		# @return [JSON] Lists all available external sources
+		def external_dbs(species = 'human', options = {})
+			return EnsemblREST.get("info/external_dbs/#{species}", {format: 'json'}.merge(options))
+		end
+		
+		# Checks if the service is alive.
+		# 
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ping
+		# @return [Boolean] True/False
+		def ping(options = {})
+			begin
+				EnsemblREST.get("info/ping", {format: 'json'}.merge(options))
+				return true
+			rescue  EnsemblREST::ServiceNotFound
+				return false
+			end
+		end
+		
+		# Shows the current version of the Ensembl REST API.
+		# 
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/rest
+		# @return [String] version of this REST server
+		def rest(options = {})
+			return EnsemblREST.get("info/rest", {format: 'json'}.merge(options))["release"]
+		end
+		
+		# Shows the current version of the Ensembl API used by the REST server.
+		# 
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/software
+		# @return [String] the current version of the Ensembl API
+		def software(options = {})
+			return EnsemblREST.get("info/software", {format: 'json'}.merge(options))["release"]
+		end
+		
+		# Lists all available species, their aliases, available adaptor groups and data release.
+		# 
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/species
+		# @return [String] Lists all available species
+		def species(options = {})
+			return EnsemblREST.get("info/species", {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/lookup.rb

@@ -0,0 +1,54 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+	module Lookup
+		module_function
+		
+		# Find the species and database for a symbol in a linked external database
+		# 
+		# @param [String] A name or symbol from an annotation source has been linked to a genetic feature
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_lookup
+		# @return [JSON] Cross references
+		def symbol(symbol, species = 'human', options = {})
+			return EnsemblREST.get("lookup/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
+		end
+		
+		# Find the species and database for a single identifier
+		# 
+		# @param [String] An Ensembl Stable ID
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup
+		# @return [JSON] Cross references
+		def id(id, options = {})
+			return EnsemblREST.get("lookup/id/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Find the species and database for a set of symbols in a linked external database. Unknown symbols are omitted from the response.
+		# 
+		# @param [String] An array of names or symbols from an annotation source has been linked to a genetic feature
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_post
+		# @return [JSON] Cross references
+		def symbol_post(symbols, species = 'human', options = {})
+			return EnsemblREST.post("lookup/symbol/#{species}", {'symbols' => symbols}, {format: 'json'}.merge(options))
+		end
+		
+		# Find the species and database for several identifiers. IDs that are not found are returned with no data.
+		# 
+		# @param [String] Ensembl Stable IDs
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup_post
+		# @return [JSON] Cross references
+		def id_post(ids, options = {})
+			return EnsemblREST.post("lookup/id", {'ids' => ids}, {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/map.rb

@@ -11,22 +11,49 @@
 
 module EnsemblREST
 	
-	module_function
-	
-	def assembly_cdna(id, region, options = {})
-		return EnsemblREST.get("map/cdna/#{id}/#{region}", {format: 'json'}.merge(options))
-	end
-	
-	def assembly_cds(id, region, options = {})
-		return EnsemblREST.get("map/cds/#{id}/#{region}", {format: 'json'}.merge(options))
-	end
-	
-	def assembly_map(species, asm_one, region, asm_two, options = {})
-		return EnsemblREST.get("map/#{species}/#{asm_one}/#{region}/#{asm_two}", {format: 'json'}.merge(options))
-	end
-	
-	def assembly_translation(id, region, options = {})
-		return EnsemblREST.get("map/translation/#{id}/#{region}", {format: 'json'}.merge(options))
+	module Map
+		module_function
+		
+		# Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
+		# 
+		# @param [String] An Ensembl stable ID
+		# @param [String] Query region
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cdna
+		# @return [JSON] genomic coordinates
+		def cdna(id, region, options = {})
+			return EnsemblREST.get("map/cdna/#{id}/#{region}", {format: 'json'}.merge(options))
+		end
+		
+		# Convert from CDS coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
+		# 
+		# @param [String] An Ensembl stable ID
+		# @param [String] Query region
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cds
+		# @return [JSON] genomic coordinates
+		def cds(id, region, options = {})
+			return EnsemblREST.get("map/cds/#{id}/#{region}", {format: 'json'}.merge(options))
+		end
+		
+		# Convert the co-ordinates of one assembly to another
+		# 
+		# @param [String] Query region
+		# @param [String] Version of the input assembly
+		# @param [String] Version of the output assembly
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_map
+		# @return [JSON] genomic coordinates
+		def map(region, asm_one, asm_two, species = 'human', options = {})
+			return EnsemblREST.get("map/#{species}/#{asm_one}/#{region}/#{asm_two}", {format: 'json'}.merge(options))
+		end
+		
+		# Convert from protein (translation) coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
+		# 
+		# @param [String] An Ensembl stable ID
+		# @param [String] Query region
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_translation
+		# @return [JSON] genomic coordinates
+		def translation(id, region, options = {})
+			return EnsemblREST.get("map/translation/#{id}/#{region}", {format: 'json'}.merge(options))
+		end
 	end
-	
 end

data/lib/ensemblrest/ontoandtaxo.rb

@@ -0,0 +1,95 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+	
+	module Ontology
+	
+		module_function
+		
+		# Reconstruct the entire ancestry of a term from is_a and part_of relationships
+		# 
+		# @param [String] An ontology term identifier
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors
+		# @return [JSON] the entire ancestry of a term
+		def ancestors(id, options = {})
+			return EnsemblREST.get("ontology/ancestors/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Reconstruct the entire ancestry of a term from is_a and part_of relationships.
+		# 
+		# @param [String] An ontology term identifier
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors_chart
+		# @return [JSON] the entire ancestry of a term
+		def ancestors_chart(id, options = {})
+			return EnsemblREST.get("ontology/ancestors/chart/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Find all the terms descended from a given term. By default searches are conducted within the namespace of the given identifier
+		# 
+		# @param [String] An ontology term identifier
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_descendants
+		# @return [JSON] the terms descended from a given term
+		def descendants(id, options = {})
+			return EnsemblREST.get("ontology/descendants/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Search for an ontological term by its namespaced identifier
+		# 
+		# @param [String] An ontology term identifier
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_id
+		# @return [JSON] an ontological term
+		def id(name, options = {})
+			return EnsemblREST.get("ontology/id/#{name}", {format: 'json'}.merge(options))
+		end
+		
+		# Search for a list of ontological terms by their name
+		# 
+		# @param [String] An ontology name. SQL wildcards are supported
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_name
+		# @return [JSON] a list of ontological terms
+		def name(name, options = {})
+			return EnsemblREST.get("ontology/name/#{URI.escape(name)}", {format: 'json'}.merge(options))
+		end
+	end
+	
+	module Taxonomy
+	
+		module_function
+	
+		# Return the taxonomic classification of a taxon node
+		# 
+		# @param [String] A taxon identifier. Can be a NCBI taxon id or a name
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_classification
+		# @return [JSON] the taxonomic classification
+		def classification(id, options = {})
+			return EnsemblREST.get("taxonomy/classification/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Search for a taxonomic term by its identifier or name
+		# 
+		# @param [String] A taxon identifier. Can be a NCBI taxon id or a name
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_id
+		# @return [JSON] the taxonomic classification
+		def id(id, options = {})
+			return EnsemblREST.get("taxonomy/id/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Search for a taxonomic id by a non-scientific name
+		# 
+		# @param [String] A non-scientific species name. Can include SQL wildcards
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_name
+		# @return [JSON] the taxonomic classification
+		def name(name, options = {})
+			return EnsemblREST.get("taxonomy/name/#{URI.escape(name)}", {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/overlap.rb

@@ -0,0 +1,47 @@
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+
+	module Overlap
+		module_function
+		
+		# Request multiple types of sequence by a list of regions.
+		# 
+		# @param [Array] Query regions. A maximum of 10Mb is allowed to be requested at any one time
+		# @param [Array] The type of feature to retrieve. Multiple values are accepted. Array of gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation, 
+		# structural_variation, somatic_structural_variation, constrained, regulatory, segmentation, motif, chipseq, array_probe
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_region
+		# @return [JSON] Requested response
+		def region(region, features = [], species = 'human', options = {})
+			return EnsemblREST.get("overlap/region/#{species}/#{region}", {format: 'json', feature: features}.merge(options))
+		end
+		
+		# Retrieves features (e.g. genes, transcripts, variations etc.) that overlap a region defined by the given identifier.
+		# 
+		# @param [String] An Ensembl stable ID
+		# @param [Array] The type of feature to retrieve. Multiple values are accepted. Array of gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation, 
+		# structural_variation, somatic_structural_variation, constrained, regulatory, segmentation, motif, chipseq, array_probe
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_id
+		# @return [JSON] Requested response
+		def id(id, features = [], options = {})
+			return EnsemblREST.get("overlap/id/#{id}", {format: 'json', feature: features}.merge(options))
+		end
+		
+		# Retrieve features related to a specific Translation as described by its stable ID (e.g. domains, variations).
+		# 
+		# @param [String] An Ensembl stable ID
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_translation
+		# @return [JSON] Requested response
+		def translation(id, options = {})
+			return EnsemblREST.get("overlap/translation/#{id}", {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/regulation.rb

@@ -0,0 +1,27 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+
+	module Regulation
+		module_function
+		
+		# Returns a RegulatoryFeature given its stable ID (e.g. ENSR00001348195)
+		# 
+		# @param [String] RegulatoryFeature stable ID
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/regulatory_id
+		# @return [JSON] the entire ancestry of a term
+		def id(id, species = 'human', options = {})
+			return EnsemblREST.get("regulatory/#{species}/#{id}", {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/sequence.rb

@@ -11,13 +11,45 @@
 
 module EnsemblREST
 	
-	module_function
-	
-	def sequence_id(id, options = {})
-		return EnsemblREST.get("sequence/id/#{id}", {format: 'fasta'}.merge(options))
-	end
-	
-	def sequence_region(region, species, options = {})
-		return EnsemblREST.get("sequence/region/#{species}/#{region}", {format: 'fasta'}.merge(options))
+	module Sequence
+		module_function
+		
+		# Request multiple types of sequence by stable identifier.
+		# 
+		# @param [String] An Ensembl stable ID
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id
+		# @return [FastaFormat] requested sequence
+		def id(id, options = {})
+			return EnsemblREST.get("sequence/id/#{id}", {format: 'fasta'}.merge(options))
+		end
+		
+		# Returns the genomic sequence of the specified region of the given species.
+		# 
+		# @param [String] Query region. A maximum of 10Mb is allowed to be requested at any one time
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region
+		# @return [FastaFormat] requested sequence
+		def region(region, species = 'human', options = {})
+			return EnsemblREST.get("sequence/region/#{species}/#{region}", {format: 'fasta'}.merge(options))
+		end
+		
+		# Request multiple types of sequence by a stable identifier list.
+		# 
+		# @param [Array] Ensembl stable IDs
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id_post
+		# @return [JSON] Requested response
+		def id_post(ids, options = {})
+			return EnsemblREST.post("sequence/id", {"ids" => ids}, {format: 'json'}.merge(options))
+		end
+		
+		# Request multiple types of sequence by a list of regions.
+		# 
+		# @param [Array] Query regions. A maximum of 10Mb is allowed to be requested at any one time
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region_post
+		# @return [JSON] Requested response
+		def region_post(regions, species = 'human', options = {})
+			return EnsemblREST.post("sequence/region/#{species}", {"regions" => regions}, {format: 'json'}.merge(options))
+		end
 	end
 end

data/lib/ensemblrest/variation.rb

@@ -0,0 +1,36 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+	
+	module Variation
+		module_function
+		
+		# Uses a variation identifier (e.g. rsID) to return the variation features
+		# 
+		# @param [String] RegulatoryFeature stable ID
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_id
+		# @return [JSON] the variation features
+		def id(id, species = 'human', options = {})
+			return EnsemblREST.get("variation/#{species}/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Uses a list of variation identifiers (e.g. rsID) to return the variation features
+		# 
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_post
+		# @return [JSON] the variation features
+		def post(ids, species = 'human', options = {})
+			return EnsemblREST.post("variation/#{species}", {"ids" => ids}, {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/variationga4gh.rb

@@ -0,0 +1,45 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+	
+	module GA4GH
+		module_function
+		
+		# Return a list of sets of genotype calls for specific samples in GA4GH format
+		# 
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gacallSet
+		# @return [JSON] a list of sets of genotype calls for specific samples
+		def gacallSet(options = {})
+			return EnsemblREST.post("ga4gh/callsets/search", {}, {format: 'json'}.merge(options))
+		end
+		
+		# Return variant call information in GA4GH format for a region on a reference sequence
+		#
+		# @param [Integer] Start position of region (zero-based, inclusive)
+		# @param [Integer] End position of region (zero-based, exclusive)
+		# @param [String] Reference sequence name
+		# @param [String] Return variant data for specific variantSets
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariants
+		# @return [JSON] variant call information in GA4GH format
+		def gavariants(start, stop, referenceName, variantSetIds, options = {})
+			return EnsemblREST.post("ga4gh/variants/search", {"variantSetIds" => variantSetIds, "referenceName" => referenceName,"start" => start ,"end" => stop}, {format: 'json'}.merge(options))
+		end
+		
+		# Return a list of variant sets in GA4GH format
+		# 
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariantset
+		# @return [JSON] a list of variant sets in GA4GH format
+		def gavariantset(options = {})
+			return EnsemblREST.post("ga4gh/variantsets/search", {}, {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/vep.rb

@@ -0,0 +1,69 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+
+	module VEP
+	
+		module_function
+		
+		# Fetch variant consequences
+		# 
+		# @param [String] Variation allele, Example Values: 'C', 'DUP'
+		# @param [String] Query region. Example Values: '9:22125503-22125502:1', '7:100318423-100321323:1'
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
+		# @return [JSON] Variants consequences
+		def region_get(allele, region, species = 'human', options = {})
+			return EnsemblREST.get("vep/#{species}/region/#{region}/#{allele}", {format: 'json'}.merge(options))
+		end
+		
+		# Fetch variant consequences based on a variation identifier
+		# 
+		# @param [String] Query ID. Supports dbSNP, COSMIC and HGMD identifiers
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
+		# @return [JSON] Variants consequences
+		def id_get(id, species = 'human', options = {})
+			return EnsemblREST.get("vep/#{species}/id/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Fetch variant consequences based on a HGVS notation
+		# 
+		# @param [String] HGVS notation. May be genomic (g), coding (c) or protein (p), with reference to chromosome name, gene name, transcript ID or protein ID.
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_hgvs_get
+		# @return [JSON] Variants consequences
+		def hgvs_get(hgvs_notation, species = 'human', options = {})
+			return EnsemblREST.get("vep/#{species}/hgvs/#{hgvs_notation}", {format: 'json'}.merge(options))
+		end
+		
+		# Fetch variant consequences for multiple ids
+		# 
+		# @param [Array] Query IDs. Supports dbSNP, COSMIC and HGMD identifiers
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_id_post
+		# @return [JSON] Variants consequences
+		def id_post(ids, species = 'human', options = {})
+			return EnsemblREST.post("vep/#{species}/id", {"ids" => ids}, {format: 'json'}.merge(options))
+		end
+		
+		# Fetch variant consequences for multiple regions
+		# 
+		# @param [Array] input lines for VEP. Example Values: ["21 26960070 rs116645811 G A . . .", "21 26965148 rs1135638 G A . . ." ]
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
+		# @return [JSON] Variants consequences
+		def region_post(variants, species = 'human', options = {})
+			return EnsemblREST.post("vep/#{species}/region", {"variants" => variants}, {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/ensemblrest/version.rb

@@ -11,5 +11,5 @@
 
 
 module EnsemblREST
-	VERSION = "0.0.5"
+	VERSION = "1.1.0"
 end

data/lib/ensemblrest/xref.rb

@@ -0,0 +1,49 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module EnsemblREST
+	
+	module Xref
+		module_function
+		
+		# Looks up an external symbol and returns all Ensembl objects linked to it. 
+		# This can be a display name for a gene/transcript/translation, a synonym or an externally linked reference. 
+		# If a gene's transcript is linked to the supplied symbol the service will return both gene and transcript (it supports transient links).
+		# 
+		# @param [String] Symbol or display name of a gene
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_external
+		# @return [JSON] Cross references
+		def external(symbol, species = 'human', options = {})
+			return EnsemblREST.get("xrefs/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
+		end
+		
+		# Perform lookups of Ensembl Identifiers and retrieve their external references in other databases
+		# 
+		# @param [String] An Ensembl Stable ID
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_id
+		# @return [JSON] Cross references
+		def id(id, options = {})
+			return EnsemblREST.get("xrefs/id/#{id}", {format: 'json'}.merge(options))
+		end
+		
+		# Performs a lookup based upon the primary accession or display label of 
+		# an external reference and returning the information we hold about the entry
+		# 
+		# @param [String] Symbol or display name of a gene
+		# @param [String] Species name/alias
+		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_name
+		# @return [JSON] Cross references
+		def name(name, species = 'human', options = {})
+			return EnsemblREST.get("xrefs/name/#{species}/#{name}", {format: 'json'}.merge(options))
+		end
+	end
+end

data/lib/test.rb

@@ -0,0 +1,129 @@
+# Bio-ensemblrest
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+require_relative 'ensemblrest'
+require_relative 'ensemblrest/connect'
+require_relative 'ensemblrest/sequence'
+require_relative 'ensemblrest/map'
+require_relative 'ensemblrest/vep'
+require_relative 'ensemblrest/overlap'
+require_relative 'ensemblrest/archive'
+require_relative 'ensemblrest/comparativegenomics'
+require_relative 'ensemblrest/xref'
+require_relative 'ensemblrest/info'
+require_relative 'ensemblrest/lookup'
+require_relative 'ensemblrest/ontoandtaxo'
+require_relative 'ensemblrest/regulation'
+require_relative 'ensemblrest/variation'
+require_relative 'ensemblrest/variationga4gh'
+
+require "test/unit"
+
+class TestEnsemblREST < Test::Unit::TestCase
+	
+	def test_archive
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Archive::id_get('ENSG00000157764')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Archive::id_post(["ENSG00000157764", "ENSG00000248378"])}
+	end
+	
+	def test_map
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::cdna("ENST00000288602", "100..300")}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::cds('ENST00000288602', '1..1000')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::map('X:1000000..1000100:1', 'GRCh37', 'GRCh38')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::translation('ENSP00000288602', '100..300')}
+	end
+	
+	def test_genetree
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genetree('ENSGT00390000003602')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genetree_member_id('ENSG00000157764')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genetree_member_symbol('BRCA2')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genomic_alignment_region('X:1000000..1000100:1')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::homology_ensemblgene('ENSG00000157764')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::homology_symbol('BRCA2')}
+	end
+	
+	def test_info
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::analysis}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::assembly_info}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::assembly_stats('X')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::biotypes}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::compara_methods}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::compara_species_sets('EPO')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::comparas}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::data}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::external_dbs}
+		assert(EnsemblREST::Info::ping)
+		assert_instance_of(String, EnsemblREST::Info::rest)
+		assert_instance_of(Fixnum, EnsemblREST::Info::software)
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::species}
+	end
+	
+	def test_lookup
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::id('ENSG00000157764')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::symbol('BRCA2')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::id_post(["ENSG00000157764", "ENSG00000248378"])}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::symbol_post(["BRCA2", "BRAF"])}
+	end
+	
+	def test_onto
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::ancestors('GO:0005667')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::ancestors_chart('GO:0005667')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::descendants('GO:0005667')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::id('GO:0005667')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::name("transcription factor complex")}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Taxonomy::classification('9606')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Taxonomy::id('9606')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Taxonomy::name('Homo%25')}
+	end
+	
+	def test_overlap
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Overlap::id('ENSG00000157764', 'gene')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Overlap::region('7:140424943-140624564', ['gene', 'transcript', 'cds', 'exon'])}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Overlap::translation('ENSP00000288602')}
+	end
+	
+	def test_regulation
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Regulation::id('ENSR00001348195')}
+	end
+	
+	def test_sequence
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::id("ENSP00000288602")}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::region("X:1000000..1000100:1", 'human')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::id_post(["ENSG00000157764", "ENSG00000248378"])}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::region_post(["X:1000000..1000100:1", "ABBA01004489.1:1..100"])}
+	end
+	
+	def test_variation
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Variation::id("rs116035550")}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Variation::post(["rs116035550", "COSM476"])}
+	end
+	
+	def test_variationga4gh
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::GA4GH::gacallSet}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::GA4GH::gavariants(17191024, 17671934, '22', [70])}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::GA4GH::gavariantset}
+	end
+	
+	def test_vep
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::hgvs_get('AGT:c.803T>C')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::id_get('COSM476')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::region_get('C', '9:22125503-22125502:1')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::id_post(["rs116035550", "COSM476" ])}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::region_post(["21  26960070  rs116645811 G A . . .", "21  26965148  rs1135638 G A . . ." ])}
+	end
+	
+	def test_xref
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Xref::external('BRCA2')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Xref::id('ENSG00000157764')}
+		assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Xref::name('BRCA2')}
+	end
+	
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ensemblrest
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 1.1.0
 platform: ruby
 authors:
 - Natapol Pornputtapong
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-14 00:00:00.000000000 Z
+date: 2015-05-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -32,10 +32,22 @@ extra_rdoc_files: []
 files:
 - ensemblrest.gemspec
 - lib/ensemblrest.rb
+- lib/ensemblrest/archive.rb
+- lib/ensemblrest/comparativegenomics.rb
 - lib/ensemblrest/connect.rb
+- lib/ensemblrest/info.rb
+- lib/ensemblrest/lookup.rb
 - lib/ensemblrest/map.rb
+- lib/ensemblrest/ontoandtaxo.rb
+- lib/ensemblrest/overlap.rb
+- lib/ensemblrest/regulation.rb
 - lib/ensemblrest/sequence.rb
+- lib/ensemblrest/variation.rb
+- lib/ensemblrest/variationga4gh.rb
+- lib/ensemblrest/vep.rb
 - lib/ensemblrest/version.rb
+- lib/ensemblrest/xref.rb
+- lib/test.rb
 homepage: http://rubygems.org/gems/ensemblrest
 licenses:
 - GPL