ensemblrest 0.0.5

checksums.yaml

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+---
+SHA1:
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+  data.tar.gz: 6b5317110ad84500394cf550835271ed6d6a7fd3
+SHA512:
+  metadata.gz: bf53774dad64eb9032f1a75f56ffe0ff98c4c4e1fa3100d868d008e0b9e0eb08df99b346b6cebfdab8477b06a69551b2f13850854c21ec9d5a2de8c7fc6a645e
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data/ensemblrest.gemspec

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+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "ensemblrest/version"
+
+Gem::Specification.new do |s|
+    s.name          = 'ensemblrest'
+    s.version       = EnsemblREST::VERSION
+    s.date          = Time.now.strftime("%Y-%m-%d")
+    s.platform      = Gem::Platform::RUBY
+    
+    s.summary       = "Ensembl REST Ruby API"
+    s.description   = "Ensembl REST Ruby API"
+    s.authors       = ["Natapol Pornputtapong"]
+    s.email         = 'natapol.por@gmail.com'
+
+    s.homepage      = 'http://rubygems.org/gems/ensemblrest'
+    s.license       = 'GPL'
+    
+    
+    s.files         = `git ls-files`.split("\n")
+    s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+    s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+    s.require_paths = ["lib"]
+    
+    s.add_dependency "bio", "~> 1.4"
+
+end

data/lib/ensemblrest.rb

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+# 
+# Bio
+# Copyright (C) 2014
+#
+# 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"
+
+$: << File.join(File.expand_path(File.dirname(__FILE__)))
+
+#Internal library
+require 'bio'
+require 'open-uri'
+require 'net/http'
+require 'uri'
+require 'json'
+require 'csv'
+require 'digest'
+
+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

data/lib/ensemblrest/connect.rb

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+# 
+# Bio-ensemblrest
+# Copyright (C) 2014
+#
+# 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
+	
+	@@url = URI.parse('http://rest.ensembl.org')
+	@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
+	
+	SUPPOTEDFORMATS = {
+		'text' => 'text/plain',
+		'fasta' => 'text/x-fasta',
+		'gff3' => 'ext/x-gff3',
+		'json' => 'application/json',
+		'msgpack' => 'application/x-msgpack',
+		'nh' => 'text/x-nh',
+		'seqxml' => 'text/x-seqxml+xml', 
+		'sereal' => 'application/x-sereal',
+		'phyloxml' => 'text/x-phyloxml+xml',
+		'xml' => 'text/xml',
+		'yaml' => 'text/x-yaml'
+	}
+		
+	
+	module_function
+	
+	def connect(server)
+		@@url = URI.parse(server)
+		@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
+	end
+	
+	def use_GRCh37
+		@@url = URI.parse('http://grch37.rest.ensembl.org/')
+		@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
+	end
+	
+	def use37
+		EnsemblREST::use_GRCh37
+	end
+	
+	def use_GRCh38
+		@@url = URI.parse('http://rest.ensembl.org/')
+		@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
+	end
+	
+	def use38
+		EnsemblREST::use_GRCh38
+	end
+	
+	def parse_options(options)
+		parsed_options = {opts: [], format: {}}
+		options.each do |k, v|
+			if k.to_s == 'format'
+				parsed_options[:format] = {'content-type' => EnsemblREST::SUPPOTEDFORMATS.has_key?(v) ? EnsemblREST::SUPPOTEDFORMATS[v] : v}
+			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"
+				else
+					"#{k}=#{v}"
+				end
+			end
+			
+		end
+		return parsed_options
+	end
+	
+	def parse_response(response, type)
+		case response.code
+		when '200'
+			case type
+			when 'application/json'
+				return JSON.parse(response.body)
+			when 'ext/x-gff3'
+				return Bio::GFF::GFF3.new(response.body)
+			when 'text/x-fasta'
+				return Bio::FastaFormat.new(response.body)
+			when 'text/x-phyloxml+xml'
+				return Bio::PhyloXML::Parser.new(response.body)
+			else
+				return response.body
+			end
+		else
+			raise "Invalid response: #{response.code}"
+		end
+	end
+	
+	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
+end

data/lib/ensemblrest/map.rb

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+# 
+# Bio-ensemblrest
+# Copyright (C) 2014
+#
+# 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_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))
+	end
+	
+end

data/lib/ensemblrest/sequence.rb

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+# 
+# Bio-ensemblrest
+# Copyright (C) 2014
+#
+# 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_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))
+	end
+end

data/lib/ensemblrest/version.rb

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+# 
+# Exodus
+# Copyright (C) 2014
+#
+# 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
+	VERSION = "0.0.5"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: ensemblrest
+version: !ruby/object:Gem::Version
+  version: 0.0.5
+platform: ruby
+authors:
+- Natapol Pornputtapong
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-04-14 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+description: Ensembl REST Ruby API
+email: natapol.por@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ensemblrest.gemspec
+- lib/ensemblrest.rb
+- lib/ensemblrest/connect.rb
+- lib/ensemblrest/map.rb
+- lib/ensemblrest/sequence.rb
+- lib/ensemblrest/version.rb
+homepage: http://rubygems.org/gems/ensemblrest
+licenses:
+- GPL
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.0.14
+signing_key: 
+specification_version: 4
+summary: Ensembl REST Ruby API
+test_files: []
+has_rdoc: