jandot-ruby-ensembl-api 0.9.2

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Files changed (33) hide show
  1. data/TUTORIAL +623 -0
  2. data/bin/ensembl +39 -0
  3. data/lib/ensembl/core/activerecord.rb +1847 -0
  4. data/lib/ensembl/core/project.rb +248 -0
  5. data/lib/ensembl/core/slice.rb +627 -0
  6. data/lib/ensembl/core/transcript.rb +425 -0
  7. data/lib/ensembl/core/transform.rb +97 -0
  8. data/lib/ensembl/db_connection.rb +148 -0
  9. data/lib/ensembl/variation/activerecord.rb +308 -0
  10. data/lib/ensembl.rb +23 -0
  11. data/samples/examples_perl_tutorial.rb +120 -0
  12. data/samples/small_example_ruby_api.rb +34 -0
  13. data/test/unit/release_45/core/run_tests.rb +12 -0
  14. data/test/unit/release_45/core/test_project.rb +235 -0
  15. data/test/unit/release_45/core/test_project_human.rb +58 -0
  16. data/test/unit/release_45/core/test_relationships.rb +61 -0
  17. data/test/unit/release_45/core/test_sequence.rb +175 -0
  18. data/test/unit/release_45/core/test_slice.rb +56 -0
  19. data/test/unit/release_45/core/test_transcript.rb +94 -0
  20. data/test/unit/release_45/core/test_transform.rb +223 -0
  21. data/test/unit/release_45/variation/test_activerecord.rb +32 -0
  22. data/test/unit/release_50/core/run_tests.rb +12 -0
  23. data/test/unit/release_50/core/test_project.rb +215 -0
  24. data/test/unit/release_50/core/test_project_human.rb +58 -0
  25. data/test/unit/release_50/core/test_relationships.rb +66 -0
  26. data/test/unit/release_50/core/test_sequence.rb +175 -0
  27. data/test/unit/release_50/core/test_slice.rb +121 -0
  28. data/test/unit/release_50/core/test_transcript.rb +108 -0
  29. data/test/unit/release_50/core/test_transform.rb +223 -0
  30. data/test/unit/release_50/variation/test_activerecord.rb +136 -0
  31. data/test/unit/test_connection.rb +58 -0
  32. data/test/unit/test_releases.rb +40 -0
  33. metadata +243 -0
data/test/unit/release_50/variation/test_activerecord.rb ADDED
@@ -0,0 +1,136 @@
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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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+
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+ require 'test/unit'
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+ require 'ensembl'
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+
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+ include Ensembl::Variation
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+
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+ DBConnection.connect('homo_sapiens')
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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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+ syn = Variation.find(27).variation_synonym
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+ assert_equal('SNP001745772',syn.name)
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+
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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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+
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+ ag = Variation.find(130).allele_groups
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+ assert_nil ag[0]
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+
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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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+
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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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+
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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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+
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+ vg = Variation.find(1352735).variation_groups
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+ assert_nil vg[0]
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+
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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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+
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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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+
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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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+
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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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+
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+ ag = Source.find(1).allele_groups
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+ assert_nil ag[0]
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+
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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
data/test/unit/test_connection.rb ADDED
@@ -0,0 +1,58 @@
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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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+
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+ require 'test/unit'
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+
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+ require 'ensembl'
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+
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+
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+ class TestConnection < Test::Unit::TestCase
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+
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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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+
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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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+
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+ def test_local_core_connection
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+
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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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+
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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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+
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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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+
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+ def test_local_variation_connection
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+
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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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+
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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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+
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+ end
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+
data/test/unit/test_releases.rb ADDED
@@ -0,0 +1,40 @@
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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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+
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+ require 'test/unit'
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+
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+ require 'ensembl'
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+
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+ include Ensembl::Core
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+
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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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+
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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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+
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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
metadata ADDED
@@ -0,0 +1,243 @@
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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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+
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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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+
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+ extra_rdoc_files:
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+ - TUTORIAL
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+ files:
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+ - bin/ensembl
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+ - lib/ensembl/core/activerecord.rb
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+ - lib/ensembl/core/project.rb
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+ - lib/ensembl/core/slice.rb
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+ - lib/ensembl/core/transcript.rb
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+ - lib/ensembl/core/transform.rb
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+ - lib/ensembl/db_connection.rb
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+ - lib/ensembl/variation/activerecord.rb
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+ - lib/ensembl.rb
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+ - samples/examples_perl_tutorial.rb
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+ - samples/small_example_ruby_api.rb
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+ - test/unit/release_45/core/run_tests.rb
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+ - test/unit/release_45/core/test_project.rb
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+ - test/unit/release_45/core/test_project_human.rb
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+ - test/unit/release_45/core/test_relationships.rb
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+ - test/unit/release_45/core/test_sequence.rb
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+ - test/unit/release_45/core/test_slice.rb
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+ - test/unit/release_45/core/test_transcript.rb
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+ - test/unit/release_45/core/test_transform.rb
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+ - test/unit/release_45/variation/test_activerecord.rb
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+ - test/unit/release_50/core/run_tests.rb
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+ - test/unit/release_50/core/test_project.rb
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+ - test/unit/release_50/core/test_project_human.rb
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+ - test/unit/release_50/core/test_relationships.rb
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+ - test/unit/release_50/core/test_sequence.rb
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+ - test/unit/release_50/core/test_slice.rb
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+ - test/unit/release_50/core/test_transcript.rb
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+ - test/unit/release_50/core/test_transform.rb
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+ - test/unit/release_50/variation/test_activerecord.rb
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+ - test/unit/test_connection.rb
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+ - test/unit/test_releases.rb
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+ - doc/classes/AssemblyExceptions.html
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+ - doc/classes/CodingPositions.html
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+ - doc/classes/CoordinateMappingsTestSimple.html
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+ - doc/classes/Ensembl/Core/Analysis.html
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+ - doc/classes/Ensembl/Core/AnalysisDescription.html
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+ - doc/classes/Ensembl/Core/AssemblyException.html
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+ - doc/classes/Ensembl/Core/AssemblyLink.html
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+ - doc/classes/Ensembl/Core/AttribType.html
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+ - doc/classes/Ensembl/Core/CoordSystem.html
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+ - doc/classes/Ensembl/Core/DBConnection.html
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+ - doc/classes/Ensembl/Core/DensityFeature.html
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+ - doc/classes/Ensembl/Core/DensityType.html
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+ - doc/classes/Ensembl/Core/Dna.html
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+ - doc/classes/Ensembl/Core/DnaAlignFeature.html
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+ - doc/classes/Ensembl/Core/Exon.html
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+ - doc/classes/Ensembl/Core/ExonStableId.html
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+ - doc/classes/Ensembl/Core/ExonSupportingFeature.html
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+ - doc/classes/Ensembl/Core/ExonTranscript.html
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+ - doc/classes/Ensembl/Core/ExternalDb.html
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+ - doc/classes/Ensembl/Core/ExternalSynonym.html
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+ - doc/classes/Ensembl/Core/Gap.html
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+ - doc/classes/Ensembl/Core/Gene.html
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+ - doc/classes/Ensembl/Core/GeneAttrib.html
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+ - doc/classes/Ensembl/Core/GeneStableId.html
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+ - doc/classes/Ensembl/Core/GoXref.html
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+ - doc/classes/Ensembl/Core/Karyotype.html
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+ - doc/classes/Ensembl/Core/Map.html
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+ - doc/classes/Ensembl/Core/Marker.html
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+ - doc/classes/Ensembl/Core/MarkerFeature.html
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+ - doc/classes/Ensembl/Core/MarkerMapLocation.html
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+ - doc/classes/Ensembl/Core/MarkerSynonym.html
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+ - doc/classes/Ensembl/Core/Meta.html
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+ - doc/classes/Ensembl/Core/MetaCoord.html
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+ - doc/classes/Ensembl/Core/MiscAttrib.html
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+ - doc/classes/Ensembl/Core/MiscFeature.html
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+ - doc/classes/Ensembl/Core/MiscFeatureMiscSet.html
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+ - doc/classes/Ensembl/Core/MiscSet.html
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+ - doc/classes/Ensembl/Core/ObjectXref.html
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+ - doc/classes/Ensembl/Core/OligoArray.html
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+ - doc/classes/Ensembl/Core/OligoFeature.html
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+ - doc/classes/Ensembl/Core/OligoProbe.html
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+ - doc/classes/Ensembl/Core/PredictionExon.html
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+ - doc/classes/Ensembl/Core/PredictionTranscript.html
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+ - doc/classes/Ensembl/Core/ProteinAlignFeature.html
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+ - doc/classes/Ensembl/Core/ProteinFeature.html
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+ - doc/classes/Ensembl/Core/RegulatoryFactor.html
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+ - doc/classes/Ensembl/Core/RegulatoryFeature.html
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+ - doc/classes/Ensembl/Core/RepeatConsensus.html
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+ - doc/classes/Ensembl/Core/RepeatFeature.html
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+ - doc/classes/Ensembl/Core/SeqRegion.html
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+ - doc/classes/Ensembl/Core/SeqRegionAttrib.html
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+ - doc/classes/Ensembl/Core/SimpleFeature.html
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+ - doc/classes/Ensembl/Core/Slice.html
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+ - doc/classes/Ensembl/Core/Sliceable.html
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+ - doc/classes/Ensembl/Core/Transcript.html
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+ - doc/classes/Ensembl/Core/TranscriptAttrib.html
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+ - doc/classes/Ensembl/Core/TranscriptStableId.html
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+ - doc/classes/Ensembl/Core/TranscriptSupportingFeature.html
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+ - doc/classes/Ensembl/Core/Translation.html
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+ - doc/classes/Ensembl/Core/TranslationAttrib.html
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+ - doc/classes/Ensembl/Core/TranslationStableId.html
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+ - doc/classes/Ensembl/Core/Xref.html
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+ - doc/classes/Ensembl/Core.html
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+ - doc/classes/Ensembl/NewDummyDBConnection.html
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+ - doc/classes/Ensembl/OldDummyDBConnection.html
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+ - doc/classes/Ensembl/Variation/Allele.html
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+ - doc/classes/Ensembl/Variation/AlleleGroup.html
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+ - doc/classes/Ensembl/Variation/DBConnection.html
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+ - doc/classes/Ensembl/Variation.html
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+ - doc/classes/Ensembl.html
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+ - doc/classes/GenomicVsCDna.html
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+ - doc/classes/GetFeatures.html
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+ - doc/classes/GetOverlappingObjects.html
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+ - doc/classes/RelationshipsTest.html
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+ - doc/classes/SequenceForCDS.html
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+ - doc/classes/SequenceForSlice.html
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+ - doc/classes/SequenceForSlicedFeature.html
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+ - doc/classes/SequenceForUnsplicedFeature.html
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+ - doc/classes/Sequences.html
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+ - doc/classes/Simple.html
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+ - doc/classes/SimpleRecordsTest.html
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+ - doc/classes/SliceMethodMissing.html
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+ - doc/classes/SliceProjectFromAssemblyToComponentForwardStrands.html
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+ - doc/classes/SliceProjectFromComponentToAssembly.html
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+ - doc/classes/SliceProjectFromComponentToAssemblyUsingTopLevel.html
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+ - doc/classes/TestConnection.html
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+ - doc/classes/TestRelease37.html
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+ - doc/classes/TestRelease45.html
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+ - doc/classes/TestRelease50.html
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+ - doc/classes/TransformFromAssemblyToComponent.html
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+ - doc/classes/TransformFromComponentToAssembly.html
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+ - doc/classes/TransformOntoSameCoordinateSystem.html
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+ - doc/files/lib/ensembl/core/activerecord_rb.html
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+ - doc/files/lib/ensembl/core/project_rb.html
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+ - doc/files/lib/ensembl/core/slice_rb.html
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+ - doc/files/lib/ensembl/core/transcript_rb.html
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+ - doc/files/lib/ensembl/core/transform_rb.html
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+ - doc/files/lib/ensembl/db_connection_rb.html
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+ - doc/files/lib/ensembl/variation/activerecord_rb.html
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+ - doc/files/lib/ensembl_rb.html
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+ - doc/files/test/unit/release_45/core/run_tests_rb.html
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+ - doc/files/test/unit/release_45/core/test_project_human_rb.html
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+ - doc/files/test/unit/release_45/core/test_project_rb.html
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+ - doc/files/test/unit/release_45/core/test_relationships_rb.html
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+ - doc/files/test/unit/release_45/core/test_sequence_rb.html
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+ - doc/files/test/unit/release_45/core/test_slice_rb.html
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+ - doc/files/test/unit/release_45/core/test_transcript_rb.html
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+ - doc/files/test/unit/release_45/core/test_transform_rb.html
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+ - doc/files/test/unit/release_45/variation/test_activerecord_rb.html
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+ - doc/files/test/unit/release_50/core/run_tests_rb.html
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+ - doc/files/test/unit/release_50/core/test_project_human_rb.html
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+ - doc/files/test/unit/release_50/core/test_project_rb.html
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+ - doc/files/test/unit/release_50/core/test_relationships_rb.html
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+ - doc/files/test/unit/release_50/core/test_sequence_rb.html
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+ - doc/files/test/unit/release_50/core/test_slice_rb.html
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+ - doc/files/test/unit/release_50/core/test_transcript_rb.html
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+ - doc/files/test/unit/release_50/core/test_transform_rb.html
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+ - doc/files/test/unit/release_50/variation/test_activerecord_rb.html
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+ - doc/files/test/unit/test_connection_rb.html
192
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+ summary: API to Ensembl databases
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+ - test/unit/test_releases.rb