jandot-ruby-ensembl-api 0.9.2
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- data/TUTORIAL +623 -0
- data/bin/ensembl +39 -0
- data/lib/ensembl/core/activerecord.rb +1847 -0
- data/lib/ensembl/core/project.rb +248 -0
- data/lib/ensembl/core/slice.rb +627 -0
- data/lib/ensembl/core/transcript.rb +425 -0
- data/lib/ensembl/core/transform.rb +97 -0
- data/lib/ensembl/db_connection.rb +148 -0
- data/lib/ensembl/variation/activerecord.rb +308 -0
- data/lib/ensembl.rb +23 -0
- data/samples/examples_perl_tutorial.rb +120 -0
- data/samples/small_example_ruby_api.rb +34 -0
- data/test/unit/release_45/core/run_tests.rb +12 -0
- data/test/unit/release_45/core/test_project.rb +235 -0
- data/test/unit/release_45/core/test_project_human.rb +58 -0
- data/test/unit/release_45/core/test_relationships.rb +61 -0
- data/test/unit/release_45/core/test_sequence.rb +175 -0
- data/test/unit/release_45/core/test_slice.rb +56 -0
- data/test/unit/release_45/core/test_transcript.rb +94 -0
- data/test/unit/release_45/core/test_transform.rb +223 -0
- data/test/unit/release_45/variation/test_activerecord.rb +32 -0
- data/test/unit/release_50/core/run_tests.rb +12 -0
- data/test/unit/release_50/core/test_project.rb +215 -0
- data/test/unit/release_50/core/test_project_human.rb +58 -0
- data/test/unit/release_50/core/test_relationships.rb +66 -0
- data/test/unit/release_50/core/test_sequence.rb +175 -0
- data/test/unit/release_50/core/test_slice.rb +121 -0
- data/test/unit/release_50/core/test_transcript.rb +108 -0
- data/test/unit/release_50/core/test_transform.rb +223 -0
- data/test/unit/release_50/variation/test_activerecord.rb +136 -0
- data/test/unit/test_connection.rb +58 -0
- data/test/unit/test_releases.rb +40 -0
- metadata +243 -0
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#
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# = test/unit/test_seq.rb - Unit test for Ensembl::Core
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#
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# Copyright:: Copyright (C) 2008
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# Jan Aerts <http://jandot.myopenid.com>
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# License:: Ruby's
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#
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# $Id:
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'ensembl'
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include Ensembl::Variation
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DBConnection.connect('homo_sapiens')
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class ActiveRecordVariation < Test::Unit::TestCase
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def test_allele
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allele = Allele.find(1)
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assert_equal('T', allele.allele)
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assert_equal(0.04, allele.frequency)
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end
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def test_allele_group
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n = AlleleGroup.count(:all)
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assert_equal(0, n)
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end
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def test_sample
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n = Sample.count(:all)
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assert_equal(12385,n)
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individual = Sample.find(5499).individual
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assert_equal('Male',individual.gender)
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i = Sample.find(6201).individual_genotype_multiple_bp
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assert_equal(1256,i.size)
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assert_equal(548383,i[0].variation_id)
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syn = Sample.find(17).sample_synonym
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assert_equal('5',syn.name)
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end
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def test_individual
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n = Individual.count(:all)
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assert_equal(7769,n)
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end
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def test_individual_genotype_multiple_bp
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n = IndividualGenotypeMultipleBp.count(:all)
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assert_equal(835033,n)
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end
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def test_compressed_genotype_single_bp
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n = CompressedGenotypeSingleBp.count(:all)
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assert_equal(12473477,n)
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end
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def test_read_coverage
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n = ReadCoverage.count(:all)
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assert_equal(9328349,n)
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end
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def test_population
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n = Population.count(:all)
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assert_equal(4616,n)
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end
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def test_variation
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n = Variation.count(:all)
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assert_equal(13383219,n)
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syn = Variation.find(27).variation_synonym
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assert_equal('SNP001745772',syn.name)
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flanking = Variation.find(130).flanking_sequence
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assert_equal(24910767,flanking.up_seq_region_start)
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assert_equal(24911281,flanking.up_seq_region_end)
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assert_equal(24911283,flanking.down_seq_region_start)
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assert_equal(24911367,flanking.down_seq_region_end)
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assert_equal(226030,flanking.seq_region_id)
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assert_equal(1,flanking.seq_region_strand)
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ag = Variation.find(130).allele_groups
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assert_nil ag[0]
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pg = Variation.find(1125).population_genotypes
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assert_equal(26,pg.size)
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assert_equal('A',pg[0].allele_1)
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assert_equal('A',pg[0].allele_2)
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assert_equal(0.2,pg[0].frequency)
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a = Variation.find(115).alleles
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assert_equal(8,a.size)
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assert_equal('C',a[0].allele)
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assert_equal(0.733,a[0].frequency)
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vf = Variation.find(5345540).variation_feature
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assert_equal('G/A',vf.allele_string)
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assert_equal('rs8175337',vf.variation_name)
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assert_equal(226028,vf.seq_region_id)
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assert_equal(10052344,vf.seq_region_start)
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assert_equal(10052344,vf.seq_region_end)
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assert_equal(1,vf.seq_region_strand)
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vg = Variation.find(1352735).variation_groups
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assert_nil vg[0]
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i = Variation.find(1352735).individual_genotype_multiple_bps
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assert_equal(31,i.size)
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end
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def test_variation_feature
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vf_sample = VariationFeature.find(4571).samples
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assert_equal(5,vf_sample.size)
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assert_equal('PERLEGEN:AFD_EUR_PANEL',vf_sample[0].name)
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end
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def test_variation_transcript
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t = Variation.find(10958566).variation_feature.transcript_variations
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assert_equal(5,t.size)
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assert_equal(69644,t[0].transcript_id)
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end
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def test_source
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syn = Source.find(1).sample_synonyms
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assert_equal('2',syn[0].name)
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ag = Source.find(1).allele_groups
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assert_nil ag[0]
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v = Source.find(6).variations
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assert_equal(19,v.size)
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assert_equal('SNP_A-8319323',v[0].name)
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end
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end
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'ensembl'
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class TestConnection < Test::Unit::TestCase
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def test_remote_core_connection
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assert_nothing_raised do
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Ensembl::Core::DBConnection.connect('homo_sapiens',46)
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end
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assert_nothing_raised do
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Ensembl::Core::DBConnection.connect('homo_sapiens',50)
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end
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end
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# This is to check if the overwrite of the default parameters is possible,
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# so you can specify an Ensembl database on a host that is different from the official Ensembl website.
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def test_local_core_connection
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# Change username, password, host and port in order to test the connection with a different Ensembl db server
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assert_nothing_raised do
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Ensembl::Core::DBConnection.connect('homo_sapiens',46,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 3306)
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end
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assert_nothing_raised do
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Ensembl::Core::DBConnection.connect('homo_sapiens',50,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 5306)
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end
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end
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def test_remote_variation_connection
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assert_nothing_raised do
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Ensembl::Variation::DBConnection.connect('homo_sapiens',46)
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end
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assert_nothing_raised do
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Ensembl::Variation::DBConnection.connect('homo_sapiens',50)
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end
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end
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def test_local_variation_connection
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# Change username, password, host and port in order to test the connection with a different Ensembl db server
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assert_nothing_raised do
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Ensembl::Variation::DBConnection.connect('homo_sapiens',46,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 3306)
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end
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assert_nothing_raised do
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Ensembl::Variation::DBConnection.connect('bos_taurus',50,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 5306)
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end
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end
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end
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'ensembl'
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include Ensembl::Core
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# Let's see if we can 'find' things
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class TestRelease45 < Test::Unit::TestCase
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def setup
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DBConnection.connect('homo_sapiens', 45)
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@slice = Slice.fetch_by_region('chromosome','1',1000,100000)
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end
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def test_gene_stable_id
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assert_equal(["ENSG00000146556", "ENSG00000177693", "ENSG00000197194", "ENSG00000197490", "ENSG00000205292"], @slice.genes.collect{|g| g.stable_id}.sort)
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end
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end
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class TestRelease37 < Test::Unit::TestCase
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def setup
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DBConnection.connect('homo_sapiens', 37)
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@slice = Slice.fetch_by_region('chromosome','1',1000,100000)
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end
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def test_gene_stable_id
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assert_equal(["ENSG00000146556", "ENSG00000177693", "ENSG00000197194", "ENSG00000197490"], @slice.genes.collect{|g| g.stable_id}.sort)
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end
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end
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class TestRelease50 < Test::Unit::TestCase
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def setup
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DBConnection.connect('homo_sapiens', 50)
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@slice = Slice.fetch_by_region('chromosome','1',1000,100000)
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end
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def test_gene_stable_id
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assert_equal(["ENSG00000146556", "ENSG00000177693", "ENSG00000197194", "ENSG00000197490", "ENSG00000205292", "ENSG00000219789", "ENSG00000221311"], @slice.genes.collect{|g| g.stable_id}.sort)
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end
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end
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metadata
ADDED
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--- !ruby/object:Gem::Specification
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name: jandot-ruby-ensembl-api
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version: !ruby/object:Gem::Version
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version: 0.9.2
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platform: ruby
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authors:
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- Jan Aerts
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autorequire: ensembl
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bindir: bin
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cert_chain: []
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date: 2009-01-11 00:00:00 -08:00
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default_executable: ensembl
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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version_requirement:
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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"
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version:
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- !ruby/object:Gem::Dependency
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name: activerecord
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version_requirement:
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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: "0"
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version:
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description: ensembl-api provides a ruby API to the Ensembl databases (http://www.ensembl.org)
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email: http://jandot.myopenid.com
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executables:
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- ensembl
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extensions: []
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39
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extra_rdoc_files:
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40
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- TUTORIAL
|
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files:
|
42
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- bin/ensembl
|
43
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- lib/ensembl/core/activerecord.rb
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44
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- lib/ensembl/core/project.rb
|
45
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- lib/ensembl/core/slice.rb
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46
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- lib/ensembl/core/transcript.rb
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47
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- lib/ensembl/core/transform.rb
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48
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- lib/ensembl/db_connection.rb
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49
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- lib/ensembl/variation/activerecord.rb
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50
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- lib/ensembl.rb
|
51
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- samples/examples_perl_tutorial.rb
|
52
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- samples/small_example_ruby_api.rb
|
53
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+
- test/unit/release_45/core/run_tests.rb
|
54
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- test/unit/release_45/core/test_project.rb
|
55
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- test/unit/release_45/core/test_project_human.rb
|
56
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- test/unit/release_45/core/test_relationships.rb
|
57
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+
- test/unit/release_45/core/test_sequence.rb
|
58
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+
- test/unit/release_45/core/test_slice.rb
|
59
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+
- test/unit/release_45/core/test_transcript.rb
|
60
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+
- test/unit/release_45/core/test_transform.rb
|
61
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+
- test/unit/release_45/variation/test_activerecord.rb
|
62
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+
- test/unit/release_50/core/run_tests.rb
|
63
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- test/unit/release_50/core/test_project.rb
|
64
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- test/unit/release_50/core/test_project_human.rb
|
65
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- test/unit/release_50/core/test_relationships.rb
|
66
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+
- test/unit/release_50/core/test_sequence.rb
|
67
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+
- test/unit/release_50/core/test_slice.rb
|
68
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+
- test/unit/release_50/core/test_transcript.rb
|
69
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+
- test/unit/release_50/core/test_transform.rb
|
70
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+
- test/unit/release_50/variation/test_activerecord.rb
|
71
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- test/unit/test_connection.rb
|
72
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+
- test/unit/test_releases.rb
|
73
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+
- doc/classes/AssemblyExceptions.html
|
74
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+
- doc/classes/CodingPositions.html
|
75
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+
- doc/classes/CoordinateMappingsTestSimple.html
|
76
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- doc/classes/Ensembl/Core/Analysis.html
|
77
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- doc/classes/Ensembl/Core/AnalysisDescription.html
|
78
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- doc/classes/Ensembl/Core/AssemblyException.html
|
79
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- doc/classes/Ensembl/Core/AssemblyLink.html
|
80
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- doc/classes/Ensembl/Core/AttribType.html
|
81
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- doc/classes/Ensembl/Core/CoordSystem.html
|
82
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- doc/classes/Ensembl/Core/DBConnection.html
|
83
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- doc/classes/Ensembl/Core/DensityFeature.html
|
84
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- doc/classes/Ensembl/Core/DensityType.html
|
85
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