ensemblrest 0.0.5
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- checksums.yaml +7 -0
- data/ensemblrest.gemspec +27 -0
- data/lib/ensemblrest.rb +38 -0
- data/lib/ensemblrest/connect.rb +109 -0
- data/lib/ensemblrest/map.rb +32 -0
- data/lib/ensemblrest/sequence.rb +23 -0
- data/lib/ensemblrest/version.rb +15 -0
- metadata +64 -0
checksums.yaml
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---
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SHA1:
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metadata.gz: a85972ee3e540b01b703eabba40b18b86a0c9846
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data.tar.gz: 6b5317110ad84500394cf550835271ed6d6a7fd3
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SHA512:
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metadata.gz: bf53774dad64eb9032f1a75f56ffe0ff98c4c4e1fa3100d868d008e0b9e0eb08df99b346b6cebfdab8477b06a69551b2f13850854c21ec9d5a2de8c7fc6a645e
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7
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data.tar.gz: 6409a4555e6acdf7ae5a455a37f54585f761a78d37abba9bd98426b7454d62431a183f7060a8512e05c6aaa47cad726661fecb6a338349d7419692a51e936633
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data/ensemblrest.gemspec
ADDED
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# -*- encoding: utf-8 -*-
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$:.push File.expand_path("../lib", __FILE__)
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require "ensemblrest/version"
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Gem::Specification.new do |s|
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s.name = 'ensemblrest'
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s.version = EnsemblREST::VERSION
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s.date = Time.now.strftime("%Y-%m-%d")
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s.platform = Gem::Platform::RUBY
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s.summary = "Ensembl REST Ruby API"
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s.description = "Ensembl REST Ruby API"
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s.authors = ["Natapol Pornputtapong"]
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s.email = 'natapol.por@gmail.com'
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s.homepage = 'http://rubygems.org/gems/ensemblrest'
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s.license = 'GPL'
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s.files = `git ls-files`.split("\n")
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s.test_files = `git ls-files -- {test,spec,features}/*`.split("\n")
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s.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
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s.require_paths = ["lib"]
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s.add_dependency "bio", "~> 1.4"
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end
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data/lib/ensemblrest.rb
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#
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# Bio
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# Copyright (C) 2014
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#
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# author: Natapol Pornputtapong <natapol.por@gmail.com>
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#
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# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
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#
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# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
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$: << File.join(File.expand_path(File.dirname(__FILE__)))
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#Internal library
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require 'bio'
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require 'open-uri'
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require 'net/http'
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require 'uri'
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require 'json'
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require 'csv'
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require 'digest'
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require 'ensemblrest/connect'
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require 'ensemblrest/sequence'
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require 'ensemblrest/map'
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require 'ensemblrest/version'
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#p EnsemblREST::sequence_id("ENSP00000288602")
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#p EnsemblREST::sequence_region("X:1000000..1000100:1", 'human')
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#
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#p EnsemblREST::assembly_cdna("ENST00000288602", "100..300")
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#p EnsemblREST::assembly_cds('ENST00000288602', '1..1000')
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#p EnsemblREST::assembly_map('human', 'GRCh37' , 'X:1000000..1000100:1', 'GRCh38')
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#p EnsemblREST::assembly_translation('ENSP00000288602', '100..300')
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#EnsemblREST.use37
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#
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#p EnsemblREST::sequence_id('ENST00000288602', type: 'cdna').seq.length
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#p EnsemblREST::sequence_id('ENST00000288602', type: 'cds').seq.length
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#
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# Bio-ensemblrest
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# Copyright (C) 2014
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#
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# author: Natapol Pornputtapong <natapol.por@gmail.com>
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#
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# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
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#
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# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
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module EnsemblREST
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@@url = URI.parse('http://rest.ensembl.org')
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@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
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SUPPOTEDFORMATS = {
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'text' => 'text/plain',
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'fasta' => 'text/x-fasta',
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'gff3' => 'ext/x-gff3',
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'json' => 'application/json',
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'msgpack' => 'application/x-msgpack',
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'nh' => 'text/x-nh',
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'seqxml' => 'text/x-seqxml+xml',
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'sereal' => 'application/x-sereal',
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'phyloxml' => 'text/x-phyloxml+xml',
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'xml' => 'text/xml',
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'yaml' => 'text/x-yaml'
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}
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module_function
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def connect(server)
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@@url = URI.parse(server)
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@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
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end
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def use_GRCh37
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@@url = URI.parse('http://grch37.rest.ensembl.org/')
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@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
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end
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def use37
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EnsemblREST::use_GRCh37
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end
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def use_GRCh38
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@@url = URI.parse('http://rest.ensembl.org/')
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@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
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end
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def use38
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EnsemblREST::use_GRCh38
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end
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def parse_options(options)
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parsed_options = {opts: [], format: {}}
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options.each do |k, v|
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if k.to_s == 'format'
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parsed_options[:format] = {'content-type' => EnsemblREST::SUPPOTEDFORMATS.has_key?(v) ? EnsemblREST::SUPPOTEDFORMATS[v] : v}
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elsif k.to_s == 'content-type'
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parsed_options[:format] = {'content-type' => v}
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else
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parsed_options[:opts].push case v.class
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when TrueClass
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"#{k}=1"
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when FalseClass
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"#{k}=0"
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else
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"#{k}=#{v}"
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end
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end
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end
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return parsed_options
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end
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def parse_response(response, type)
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case response.code
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when '200'
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case type
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when 'application/json'
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return JSON.parse(response.body)
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when 'ext/x-gff3'
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return Bio::GFF::GFF3.new(response.body)
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when 'text/x-fasta'
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return Bio::FastaFormat.new(response.body)
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when 'text/x-phyloxml+xml'
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return Bio::PhyloXML::Parser.new(response.body)
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else
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return response.body
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end
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else
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raise "Invalid response: #{response.code}"
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end
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end
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def get(get_path, options)
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parsed_options = EnsemblREST::parse_options(options)
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request = Net::HTTP::Get.new("#{get_path}#{parsed_options[:opts].empty? ? '' : "?#{parsed_options[:opts].join(';')}"}", parsed_options[:format])
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return EnsemblREST::parse_response(@@http_connect.request(request), parsed_options[:format]['content-type'])
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end
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#def post(get_path, request_body, options)
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# request = Net::HTTP::Get.new(get_path, EnsemblREST::parse_format(options))
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# return EnsemblREST::parse_response(@@http_connect.request(request), options['Content-Type'])
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#end
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end
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#
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# Bio-ensemblrest
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# Copyright (C) 2014
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#
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# author: Natapol Pornputtapong <natapol.por@gmail.com>
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#
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# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
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#
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# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
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module EnsemblREST
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module_function
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def assembly_cdna(id, region, options = {})
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return EnsemblREST.get("map/cdna/#{id}/#{region}", {format: 'json'}.merge(options))
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end
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def assembly_cds(id, region, options = {})
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return EnsemblREST.get("map/cds/#{id}/#{region}", {format: 'json'}.merge(options))
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end
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def assembly_map(species, asm_one, region, asm_two, options = {})
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return EnsemblREST.get("map/#{species}/#{asm_one}/#{region}/#{asm_two}", {format: 'json'}.merge(options))
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end
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def assembly_translation(id, region, options = {})
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return EnsemblREST.get("map/translation/#{id}/#{region}", {format: 'json'}.merge(options))
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end
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end
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#
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# Bio-ensemblrest
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# Copyright (C) 2014
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#
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# author: Natapol Pornputtapong <natapol.por@gmail.com>
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#
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# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
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#
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# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
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module EnsemblREST
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module_function
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def sequence_id(id, options = {})
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return EnsemblREST.get("sequence/id/#{id}", {format: 'fasta'}.merge(options))
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end
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def sequence_region(region, species, options = {})
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return EnsemblREST.get("sequence/region/#{species}/#{region}", {format: 'fasta'}.merge(options))
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end
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end
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#
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# Exodus
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# Copyright (C) 2014
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#
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# author: Natapol Pornputtapong <natapol.por@gmail.com>
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#
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# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
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#
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# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
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module EnsemblREST
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VERSION = "0.0.5"
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end
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metadata
ADDED
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--- !ruby/object:Gem::Specification
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name: ensemblrest
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version: !ruby/object:Gem::Version
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version: 0.0.5
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platform: ruby
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authors:
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- Natapol Pornputtapong
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2015-04-14 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.4'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.4'
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description: Ensembl REST Ruby API
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email: natapol.por@gmail.com
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executables: []
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extensions: []
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extra_rdoc_files: []
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files:
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- ensemblrest.gemspec
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- lib/ensemblrest.rb
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- lib/ensemblrest/connect.rb
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- lib/ensemblrest/map.rb
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- lib/ensemblrest/sequence.rb
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- lib/ensemblrest/version.rb
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homepage: http://rubygems.org/gems/ensemblrest
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licenses:
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- GPL
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metadata: {}
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
|
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.0.14
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signing_key:
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specification_version: 4
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summary: Ensembl REST Ruby API
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test_files: []
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has_rdoc:
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