bio-ensembl-rest 0.1.0 → 0.2.0
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- data/.travis.yml +0 -1
- data/README.md +3 -3
- data/Rakefile +1 -1
- data/lib/bio-ensembl-rest/comparative-genomics.rb +32 -0
- data/lib/bio-ensembl-rest/ensembl-rest-main.rb +0 -2
- data/lib/bio-ensembl-rest/features.rb +17 -0
- data/lib/bio-ensembl-rest/information.rb +64 -0
- data/test/test-comparative-genomics.rb +37 -0
- data/test/test-cross-reference.rb +2 -0
- data/test/test-features.rb +17 -0
- data/test/test-information.rb +73 -0
- data/test/test-lookup.rb +2 -0
- data/test/test-mapping.rb +2 -0
- data/test/test-ontologies.rb +4 -0
- data/test/test-sequence.rb +5 -10
- data/test/test-taxonomy.rb +2 -0
- data/test/test-variation.rb +2 -0
- metadata +30 -13
- checksums.yaml +0 -7
data/.travis.yml
CHANGED
data/README.md
CHANGED
@@ -3,13 +3,13 @@ Ensembl Rest
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A Ruby library for the RESTful Ensembl API.
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[![
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[![Gem Version](https://badge.fury.io/rb/bio-ensembl-rest.png)](http://badge.fury.io/rb/bio-ensembl-rest)
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Obtaining
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---------
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```sh
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gem install ensembl-rest
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gem install bio-ensembl-rest
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```
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for the repository:
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```sh
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@@ -43,7 +43,7 @@ See the [ensembl-rest wiki page](https://github.com/ALTree/bio-ensembl-rest/wiki
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### version-specific issues
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-
* On jruby
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+
* On jruby, methods in the ComparativeGenomics module fail if called with `response: ruby`,
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due to a C dependency in the 'bio' gem.
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* On rubinius, methods in the ComparativeGenomics module fail if called with `response: ruby`,
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data/Rakefile
CHANGED
@@ -14,7 +14,7 @@ require 'rake'
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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gem.name = "bio-ensembl-rest"
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-
gem.version = '0.
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gem.version = '0.2.0'
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gem.homepage = "http://github.com/ALTree/bio-ensembl-rest"
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gem.license = "MIT"
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gem.summary = "Ruby Ensembl REST api"
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@@ -1,6 +1,38 @@
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1
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module EnsemblRest
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module ComparativeGenomics
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##
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# Retrieves genomic alignments as separate blocks based on its location
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def self.alignment_block(species, region, opts = {})
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opts = EnsemblRest.parse_options opts
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path = EnsemblRest.build_path "/alignment/block/region/#{species}/#{region}", opts
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+
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if opts['content-type'] == 'ruby'
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plain_opts = opts.clone
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plain_opts['content-type'] = 'application/json'
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return JSON.parse ComparativeGenomics.alignment_block species, region, plain_opts
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end
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return EnsemblRest.fetch_data path, opts, 'compara'
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end
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##
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# Retrieves genomic alignments as a single slice based on its location
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def self.alignment_slice(species, region, opts = {})
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opts = EnsemblRest.parse_options opts
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path = EnsemblRest.build_path "/alignment/slice/region/#{species}/#{region}", opts
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if opts['content-type'] == 'ruby'
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plain_opts = opts.clone
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plain_opts['content-type'] = 'application/json'
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return JSON.parse ComparativeGenomics.alignment_slice species, region, plain_opts
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end
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return EnsemblRest.fetch_data path, opts, 'compara'
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end
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##
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# Retrieves Gene Tree dumps for a given Gene Tree stable identifier
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def self.genetree_id(id, opts = {})
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@@ -52,7 +52,6 @@ module EnsemblRest
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opts
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end
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-
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## HTTP request stuff ##
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def self.build_path(home, opts) # :nodoc:
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@@ -62,7 +61,6 @@ module EnsemblRest
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URI::encode path
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end
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-
# TODO: add tests to check if this default stuff is ok
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def self.fetch_data(path, opts, mod) # :nodoc:
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# what we should set as content-type in the header
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# to keep ensembl happy when the the user does not
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@@ -42,5 +42,22 @@ module EnsemblRest
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return EnsemblRest.fetch_data path, opts, 'features'
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end
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##
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# Uses the given identifier to return translation related features.
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def self.feature_translation(id, opts = {})
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opts = EnsemblRest.parse_options opts
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path = EnsemblRest.build_path "/feature/translation/#{id}", opts
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if opts['content-type'] == 'ruby'
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plain_opts = opts.clone
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plain_opts['content-type'] = 'application/json'
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return JSON.parse feature_translation id, plain_opts
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end
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return EnsemblRest.fetch_data path, opts, 'features'
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end
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end
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end
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@@ -33,6 +33,70 @@ module EnsemblRest
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end
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##
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# Lists the available analyses by logic name and the database type those logic names are found in.
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def self.info_analysis(species, opts = {})
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opts = EnsemblRest.parse_options opts
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path = EnsemblRest.build_path "/info/analysis/#{species}", opts
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+
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if opts['content-type'] == 'ruby'
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plain_opts = opts.clone
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plain_opts['content-type'] = 'application/json'
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return JSON.parse info_analysis species, plain_opts
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end
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return EnsemblRest.fetch_data path, opts, 'information'
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end
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##
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# Lists all available biotypes for the given species.
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def self.info_biotypes(species, opts = {})
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opts = EnsemblRest.parse_options opts
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path = EnsemblRest.build_path "/info/biotypes/#{species}", opts
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if opts['content-type'] == 'ruby'
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plain_opts = opts.clone
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plain_opts['content-type'] = 'application/json'
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return JSON.parse info_biotypes species, plain_opts
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end
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return EnsemblRest.fetch_data path, opts, 'information'
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end
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##
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68
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#
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def self.info_compara_methods(opts = {})
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opts = EnsemblRest.parse_options opts
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path = EnsemblRest.build_path "/info/compara/methods", opts
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if opts['content-type'] == 'ruby'
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plain_opts = opts.clone
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plain_opts['content-type'] = 'application/json'
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return JSON.parse info_compara_methods plain_opts
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+
end
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+
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return EnsemblRest.fetch_data path, opts, 'information'
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end
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+
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+
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+
##
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#
|
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def self.info_compara_species_sets_method(method, opts = {})
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opts = EnsemblRest.parse_options opts
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path = EnsemblRest.build_path "/info/compara/species_sets/#{method}", opts
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+
|
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if opts['content-type'] == 'ruby'
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plain_opts = opts.clone
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plain_opts['content-type'] = 'application/json'
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return JSON.parse info_compara_species_sets_method method, plain_opts
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end
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return EnsemblRest.fetch_data path, opts, 'information'
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end
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##
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# Lists all available comparative genomics databases and their data release
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def self.info_comparas(opts = {})
|
@@ -2,6 +2,37 @@ require_relative 'helper'
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2
2
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3
3
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class TestComparativeGenomics < Test::Unit::TestCase
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4
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context 'alignment_block' do
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setup do
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EnsemblRest.connect_db
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end
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should 'support a basic call and return the correct data' do
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align = ComparativeGenomics.alignment_block 'homo sapiens', '2:106040000-106040050:1'
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assert align.index 'GTAGCAGGAAGAATGTTTATCTCTGTGTCTTGTCTTTCTGGTTAAAGGTAT'
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end
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sleep(1)
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end
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context 'alignment_slice' do
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setup do
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EnsemblRest.connect_db
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end
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should 'support a basic call and return the correct data' do
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align = ComparativeGenomics.alignment_slice 'homo sapiens', '2:106040000-106040050:1'
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assert align.index 'GTAGCAGGAAGAATGTTTATCTCTGTGTCTTGTCTTTCTGGTTAAAGGTAT'
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end
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+
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end
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context 'genetree_id' do
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setup do
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@@ -13,6 +44,8 @@ class TestComparativeGenomics < Test::Unit::TestCase
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assert tree.index('Euteleostomi') && tree.index('Sarcopterygii')
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end
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sleep(1)
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should 'work with nh response type' do
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tree1 = ComparativeGenomics.genetree_id 'ENSGT00390000003602',
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response: 'nh',
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@@ -25,6 +58,8 @@ class TestComparativeGenomics < Test::Unit::TestCase
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assert tree2.index 'xiphophorus_maculatus'
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end
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sleep(1)
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should 'return a Bio::PhyloXML object' do
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tree = ComparativeGenomics.genetree_id 'ENSGT00390000003602',
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response: 'ruby'
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@@ -94,6 +129,8 @@ class TestComparativeGenomics < Test::Unit::TestCase
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assert_nothing_raised { JSON.parse hom }
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end
|
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sleep(1)
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+
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should 'return a xml object' do
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hom = ComparativeGenomics.homology_id 'ENSG00000157764',
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response: 'xml'
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data/test/test-features.rb
CHANGED
@@ -23,6 +23,8 @@ class TestFeatures < Test::Unit::TestCase
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end
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end
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sleep(1)
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should 'raise error if no feature is given' do
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assert_raises RuntimeError do
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Features.feature_id 'ENSG00000157764', response: 'json'
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@@ -54,6 +56,8 @@ class TestFeatures < Test::Unit::TestCase
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assert fts.index '140624564' # gene end here
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end
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59
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+
sleep(1)
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60
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+
|
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should 'support multiple features' do
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58
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assert_nothing_raised do
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63
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Features.feature_region 'human', '7:140424943-140624564',
|
@@ -72,5 +76,18 @@ class TestFeatures < Test::Unit::TestCase
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76
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end
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79
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+
context 'feature_translation' do
|
80
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+
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81
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setup do
|
82
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EnsemblRest.connect_db
|
83
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+
end
|
84
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+
|
85
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should 'support a basic call and return the correct data' do
|
86
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+
ft = Features.feature_translation 'ENSP00000288602'
|
87
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+
assert ft.index('SSF56112')
|
88
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+
end
|
89
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+
|
90
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+
end
|
91
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+
|
75
92
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|
76
93
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end
|
data/test/test-information.rb
CHANGED
@@ -32,8 +32,75 @@ class TestInformation < Test::Unit::TestCase
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32
32
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assert info.index 'chromosome' # coordinate_system should be this
|
33
33
|
end
|
34
34
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35
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+
sleep(1)
|
36
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+
|
35
37
|
end
|
36
38
|
|
39
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+
context 'info_analysis' do
|
40
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+
|
41
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+
setup do
|
42
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+
EnsemblRest.connect_db
|
43
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+
end
|
44
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+
|
45
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+
should 'support a basic call and return the correct data' do
|
46
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+
assert_nothing_raised do
|
47
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+
info = Information.info_analysis 'homo sapiens'
|
48
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+
end
|
49
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+
end
|
50
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+
|
51
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+
sleep(1)
|
52
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+
|
53
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+
end
|
54
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+
|
55
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+
context 'info_biotypes' do
|
56
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+
|
57
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+
setup do
|
58
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+
EnsemblRest.connect_db
|
59
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+
end
|
60
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+
|
61
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+
should 'support a basic call and return the correct data' do
|
62
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+
assert_nothing_raised do
|
63
|
+
info = Information.info_biotypes 'homo sapiens'
|
64
|
+
end
|
65
|
+
end
|
66
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+
|
67
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+
sleep(1)
|
68
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+
|
69
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+
end
|
70
|
+
|
71
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+
context 'info_compara_methods' do
|
72
|
+
|
73
|
+
setup do
|
74
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+
EnsemblRest.connect_db
|
75
|
+
end
|
76
|
+
|
77
|
+
should 'support a basic call and return the correct data' do
|
78
|
+
assert_nothing_raised do
|
79
|
+
info = Information.info_compara_methods
|
80
|
+
end
|
81
|
+
end
|
82
|
+
|
83
|
+
sleep(1)
|
84
|
+
|
85
|
+
end
|
86
|
+
|
87
|
+
context 'info_compara_species_sets_method' do
|
88
|
+
|
89
|
+
setup do
|
90
|
+
EnsemblRest.connect_db
|
91
|
+
end
|
92
|
+
|
93
|
+
should 'support a basic call and return the correct data' do
|
94
|
+
assert_nothing_raised do
|
95
|
+
info = Information.info_compara_species_sets_method 'EPO'
|
96
|
+
end
|
97
|
+
end
|
98
|
+
|
99
|
+
sleep(1)
|
100
|
+
|
101
|
+
end
|
102
|
+
|
103
|
+
|
37
104
|
|
38
105
|
context 'info_comparas' do
|
39
106
|
|
@@ -48,6 +115,8 @@ class TestInformation < Test::Unit::TestCase
|
|
48
115
|
assert info.index 'release' # number of the databases
|
49
116
|
end
|
50
117
|
|
118
|
+
sleep(1)
|
119
|
+
|
51
120
|
end
|
52
121
|
|
53
122
|
|
@@ -79,6 +148,8 @@ class TestInformation < Test::Unit::TestCase
|
|
79
148
|
assert info.index '1' # so we know the server is alive
|
80
149
|
end
|
81
150
|
|
151
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+
sleep(1)
|
152
|
+
|
82
153
|
end
|
83
154
|
|
84
155
|
|
@@ -93,6 +164,8 @@ class TestInformation < Test::Unit::TestCase
|
|
93
164
|
assert info.index 'release' # we expect a release number
|
94
165
|
end
|
95
166
|
|
167
|
+
sleep(1)
|
168
|
+
|
96
169
|
end
|
97
170
|
|
98
171
|
|
data/test/test-lookup.rb
CHANGED
@@ -16,6 +16,8 @@ class TestLookup < Test::Unit::TestCase
|
|
16
16
|
assert look.index 'ENSG00000157764' # exactly this one
|
17
17
|
end
|
18
18
|
|
19
|
+
sleep(1)
|
20
|
+
|
19
21
|
should 'support the full parameter' do
|
20
22
|
look_plain = Lookup.lookup_id 'ENSG00000157764'
|
21
23
|
look_full = Lookup.lookup_id 'ENSG00000157764', format: 'full'
|
data/test/test-mapping.rb
CHANGED
data/test/test-ontologies.rb
CHANGED
@@ -61,6 +61,8 @@ class TestOntologies < Test::Unit::TestCase
|
|
61
61
|
assert ont.index 'GO:0043231' # and this one, too
|
62
62
|
end
|
63
63
|
|
64
|
+
sleep(1)
|
65
|
+
|
64
66
|
should 'support the subset parameter' do
|
65
67
|
ont1 = Ontologies.ontology_descendents 'GO:0005667', subset: 'goslim_generic'
|
66
68
|
ont2 = Ontologies.ontology_descendents 'GO:0005667'
|
@@ -85,6 +87,8 @@ class TestOntologies < Test::Unit::TestCase
|
|
85
87
|
assert ont.index 'GO:0044451' # his parent
|
86
88
|
end
|
87
89
|
|
90
|
+
sleep(1)
|
91
|
+
|
88
92
|
should 'return a ruby object' do
|
89
93
|
ont = Ontologies.ontology_id 'GO:0005667', response: 'ruby'
|
90
94
|
assert_instance_of Hash, ont
|
data/test/test-sequence.rb
CHANGED
@@ -15,6 +15,8 @@ class TestSequence < Test::Unit::TestCase
|
|
15
15
|
assert_equal seq2.size, 18
|
16
16
|
end
|
17
17
|
|
18
|
+
sleep(1)
|
19
|
+
|
18
20
|
should 'expand the sequence 10 pairs upstream' do
|
19
21
|
seq1 = Sequence.sequence_id 'ENSE00001154485',
|
20
22
|
response: 'text',
|
@@ -35,16 +37,7 @@ class TestSequence < Test::Unit::TestCase
|
|
35
37
|
assert_instance_of Bio::Sequence, seq
|
36
38
|
end
|
37
39
|
|
38
|
-
|
39
|
-
assert_raises RuntimeError do
|
40
|
-
Sequence.sequence_id 'CCDS5863.1',
|
41
|
-
response: 'fasta',
|
42
|
-
object_type: 'transcript',
|
43
|
-
db_type: 'otherfeatures',
|
44
|
-
type: 'cds',
|
45
|
-
species: 'human'
|
46
|
-
end
|
47
|
-
end
|
40
|
+
sleep(1)
|
48
41
|
|
49
42
|
should 'return multiple sequences' do
|
50
43
|
response = Sequence.sequence_id 'ENSG00000157764',
|
@@ -97,6 +90,8 @@ class TestSequence < Test::Unit::TestCase
|
|
97
90
|
assert_nothing_raised { JSON.parse seq }
|
98
91
|
end
|
99
92
|
|
93
|
+
sleep(1)
|
94
|
+
|
100
95
|
should 'return a Bio::Sequence object' do
|
101
96
|
seq = Sequence.sequence_region 'human',
|
102
97
|
'X:1000000..1000100:1',
|
data/test/test-taxonomy.rb
CHANGED
data/test/test-variation.rb
CHANGED
metadata
CHANGED
@@ -1,60 +1,68 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bio-ensembl-rest
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.2.0
|
5
|
+
prerelease:
|
5
6
|
platform: ruby
|
6
7
|
authors:
|
7
8
|
- Alberto Donizetti
|
8
9
|
autorequire:
|
9
10
|
bindir: bin
|
10
11
|
cert_chain: []
|
11
|
-
date: 2013-
|
12
|
+
date: 2013-09-27 00:00:00.000000000 Z
|
12
13
|
dependencies:
|
13
14
|
- !ruby/object:Gem::Dependency
|
14
15
|
name: bio
|
15
16
|
requirement: !ruby/object:Gem::Requirement
|
17
|
+
none: false
|
16
18
|
requirements:
|
17
|
-
- - '>='
|
19
|
+
- - ! '>='
|
18
20
|
- !ruby/object:Gem::Version
|
19
21
|
version: 1.4.3
|
20
22
|
type: :runtime
|
21
23
|
prerelease: false
|
22
24
|
version_requirements: !ruby/object:Gem::Requirement
|
25
|
+
none: false
|
23
26
|
requirements:
|
24
|
-
- - '>='
|
27
|
+
- - ! '>='
|
25
28
|
- !ruby/object:Gem::Version
|
26
29
|
version: 1.4.3
|
27
30
|
- !ruby/object:Gem::Dependency
|
28
31
|
name: libxml-ruby
|
29
32
|
requirement: !ruby/object:Gem::Requirement
|
33
|
+
none: false
|
30
34
|
requirements:
|
31
|
-
- - '>='
|
35
|
+
- - ! '>='
|
32
36
|
- !ruby/object:Gem::Version
|
33
37
|
version: '2'
|
34
38
|
type: :runtime
|
35
39
|
prerelease: false
|
36
40
|
version_requirements: !ruby/object:Gem::Requirement
|
41
|
+
none: false
|
37
42
|
requirements:
|
38
|
-
- - '>='
|
43
|
+
- - ! '>='
|
39
44
|
- !ruby/object:Gem::Version
|
40
45
|
version: '2'
|
41
46
|
- !ruby/object:Gem::Dependency
|
42
47
|
name: shoulda
|
43
48
|
requirement: !ruby/object:Gem::Requirement
|
49
|
+
none: false
|
44
50
|
requirements:
|
45
|
-
- - '>='
|
51
|
+
- - ! '>='
|
46
52
|
- !ruby/object:Gem::Version
|
47
53
|
version: '0'
|
48
54
|
type: :development
|
49
55
|
prerelease: false
|
50
56
|
version_requirements: !ruby/object:Gem::Requirement
|
57
|
+
none: false
|
51
58
|
requirements:
|
52
|
-
- - '>='
|
59
|
+
- - ! '>='
|
53
60
|
- !ruby/object:Gem::Version
|
54
61
|
version: '0'
|
55
62
|
- !ruby/object:Gem::Dependency
|
56
63
|
name: rdoc
|
57
64
|
requirement: !ruby/object:Gem::Requirement
|
65
|
+
none: false
|
58
66
|
requirements:
|
59
67
|
- - ~>
|
60
68
|
- !ruby/object:Gem::Version
|
@@ -62,6 +70,7 @@ dependencies:
|
|
62
70
|
type: :development
|
63
71
|
prerelease: false
|
64
72
|
version_requirements: !ruby/object:Gem::Requirement
|
73
|
+
none: false
|
65
74
|
requirements:
|
66
75
|
- - ~>
|
67
76
|
- !ruby/object:Gem::Version
|
@@ -69,6 +78,7 @@ dependencies:
|
|
69
78
|
- !ruby/object:Gem::Dependency
|
70
79
|
name: bundler
|
71
80
|
requirement: !ruby/object:Gem::Requirement
|
81
|
+
none: false
|
72
82
|
requirements:
|
73
83
|
- - ~>
|
74
84
|
- !ruby/object:Gem::Version
|
@@ -76,6 +86,7 @@ dependencies:
|
|
76
86
|
type: :development
|
77
87
|
prerelease: false
|
78
88
|
version_requirements: !ruby/object:Gem::Requirement
|
89
|
+
none: false
|
79
90
|
requirements:
|
80
91
|
- - ~>
|
81
92
|
- !ruby/object:Gem::Version
|
@@ -83,6 +94,7 @@ dependencies:
|
|
83
94
|
- !ruby/object:Gem::Dependency
|
84
95
|
name: jeweler
|
85
96
|
requirement: !ruby/object:Gem::Requirement
|
97
|
+
none: false
|
86
98
|
requirements:
|
87
99
|
- - ~>
|
88
100
|
- !ruby/object:Gem::Version
|
@@ -90,6 +102,7 @@ dependencies:
|
|
90
102
|
type: :development
|
91
103
|
prerelease: false
|
92
104
|
version_requirements: !ruby/object:Gem::Requirement
|
105
|
+
none: false
|
93
106
|
requirements:
|
94
107
|
- - ~>
|
95
108
|
- !ruby/object:Gem::Version
|
@@ -133,25 +146,29 @@ files:
|
|
133
146
|
homepage: http://github.com/ALTree/bio-ensembl-rest
|
134
147
|
licenses:
|
135
148
|
- MIT
|
136
|
-
metadata: {}
|
137
149
|
post_install_message:
|
138
150
|
rdoc_options: []
|
139
151
|
require_paths:
|
140
152
|
- lib
|
141
153
|
required_ruby_version: !ruby/object:Gem::Requirement
|
154
|
+
none: false
|
142
155
|
requirements:
|
143
|
-
- - '>='
|
156
|
+
- - ! '>='
|
144
157
|
- !ruby/object:Gem::Version
|
145
158
|
version: '0'
|
159
|
+
segments:
|
160
|
+
- 0
|
161
|
+
hash: -796222272840481707
|
146
162
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
163
|
+
none: false
|
147
164
|
requirements:
|
148
|
-
- - '>='
|
165
|
+
- - ! '>='
|
149
166
|
- !ruby/object:Gem::Version
|
150
167
|
version: '0'
|
151
168
|
requirements: []
|
152
169
|
rubyforge_project:
|
153
|
-
rubygems_version:
|
170
|
+
rubygems_version: 1.8.25
|
154
171
|
signing_key:
|
155
|
-
specification_version:
|
172
|
+
specification_version: 3
|
156
173
|
summary: Ruby Ensembl REST api
|
157
174
|
test_files: []
|
checksums.yaml
DELETED
@@ -1,7 +0,0 @@
|
|
1
|
-
---
|
2
|
-
SHA1:
|
3
|
-
metadata.gz: e112aedd2a2a78c4f241301731d39e2a3f094942
|
4
|
-
data.tar.gz: 483b616adf1743cac1b35088b59fa4d68e85e915
|
5
|
-
SHA512:
|
6
|
-
metadata.gz: 7fa0521d7923a7b9aafe1427258037a27b3794c736f36b9c0bec00d2b68b051b22195abbb3bec34307735a8274fcd9e58bfbb55b02ca2db745f76748f19dd90c
|
7
|
-
data.tar.gz: f91ecf17d9f0a267851e936efa1d4522160d54b56ba892ef1c2ad7f659f8fcdd1e1ed0a1301cc464f519566eedaf1c5894292791acc31144116dc68caf4cb07f
|