ruby-ensembl-api 0.9.6

data/test/unit/release_56/core/test_slice.rb

@@ -0,0 +1,54 @@
+#
+# = test/unit/release_53/core/test_slice.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2009
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+# License::     Ruby's
+#
+# $Id:
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'lib/ensembl'
+
+include Ensembl::Core
+
+class TestSlice < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.connect('homo_sapiens', 56)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_forward
+    seq1 = "GGCCAAGCTGGTCTCAAACTCCTGACCTCGTGATCCGCCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGGGCCACTGGGTCCGGCCGCATGTCTGGCTAATTTTGTAGAGACAGGGCCTCCCTATACTGCCCAGGCTGGTTTCAAGCTCCTGGCTTCAAGGGGTCCTCCTGCCTTGGCCTCCCGAAGTGCTGG"
+    s = Slice.fetch_by_region("chromosome","13",31786617,31786816,1)
+    assert_equal(seq1,s.seq.upcase)
+    assert_equal("13",s.seq_region.name)
+    assert_equal(31786617,s.start)
+    assert_equal(31786816,s.stop)
+  end
+  
+  def test_reverse
+    seq2 = "CCAGCACTTCGGGAGGCCAAGGCAGGAGGACCCCTTGAAGCCAGGAGCTTGAAACCAGCCTGGGCAGTATAGGGAGGCCCTGTCTCTACAAAATTAGCCAGACATGCGGCCGGACCCAGTGGCCCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCACGAGGTCAGGAGTTTGAGACCAGCTTGGCC"
+    s_rev = Slice.fetch_by_region("chromosome","13",31786617,31786816,-1)
+    assert_equal(seq2,s_rev.seq.upcase)
+    assert_equal("13",s_rev.seq_region.name)
+    assert_equal(31786617,s_rev.start)
+    assert_equal(31786816,s_rev.stop)
+  end
+
+  def test_slice_genes
+  	slice = Slice.fetch_by_region("chromosome","13",31773073,31909413,1)
+	genes = slice.genes
+	assert_equal("ENSG00000229427",genes[1].stable_id)
+  	assert_equal("ENSG00000187676",genes[0].stable_id)
+  end
+
+end

data/test/unit/release_56/core/test_transform.rb

@@ -0,0 +1,63 @@
+#
+# = test/unit/release_53/core/test_transform.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2009
+#               Jan Aerts <http://jandot.myopenid.com>
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+# License::     Ruby's
+#
+# $Id:
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+
+require 'lib/ensembl'
+
+include Ensembl::Core
+
+
+# For all tests, the source (i.e. the seq_region that the feature is annotated
+# on initially) remains forward.
+#
+# Same coordinate system: test names refer to direction of gene vs chromosome
+class TransformOntoSameCoordinateSystem < Test::Unit::TestCase
+
+  def setup
+    DBConnection.connect('homo_sapiens', 56)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+
+  def test_rev
+    source_gene = Gene.find_by_stable_id("ENSG00000165322")
+    target_gene = source_gene.transform('chromosome')
+
+    assert_equal('10', source_gene.seq_region.name)
+    assert_equal(32094365, source_gene.seq_region_start)
+    assert_equal(32217770, source_gene.seq_region_end)
+    assert_equal(-1, source_gene.seq_region_strand)
+    assert_equal('10', target_gene.seq_region.name)
+    assert_equal(32094365, target_gene.seq_region_start)
+    assert_equal(32217770, target_gene.seq_region_end)
+    assert_equal(-1, target_gene.seq_region_strand)
+  end
+
+  def test_fw
+    source_gene = Gene.find_by_stable_id("ENSG00000133401")
+    target_gene = source_gene.transform('chromosome')
+    assert_equal('5', source_gene.seq_region.name)
+    assert_equal(31639517, source_gene.seq_region_start)
+    assert_equal(32111037, source_gene.seq_region_end)
+    assert_equal(1, source_gene.seq_region_strand)
+    assert_equal('5', target_gene.seq_region.name)
+    assert_equal(31639517, target_gene.seq_region_start)
+    assert_equal(32111037, target_gene.seq_region_end)
+    assert_equal(1, target_gene.seq_region_strand)
+  end
+
+end

data/test/unit/release_56/variation/test_activerecord.rb

@@ -0,0 +1,142 @@
+#
+# = test/unit/release_50/variation/test_activerecord.rb - Unit test for Ensembl::Variation
+#
+# Copyright::   Copyright (C) 2009
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+#
+# License::     Ruby's
+#
+# $Id:
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'lib/ensembl'
+
+include Ensembl::Variation
+
+class ActiveRecordVariation < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.connect('homo_sapiens',56)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_allele
+    allele = Allele.find(1)
+    assert_equal('T', allele.allele)
+    assert_equal(0.04, allele.frequency)
+  end
+
+  def test_sample
+    n = Sample.count(:all)
+    assert_equal(17822,n)
+    individual = Sample.find(12468).individual
+    assert_equal('Male',individual.gender)
+    i = Sample.find(13131).individual_genotype_multiple_bp
+    assert_equal(3,i.size)
+    assert_equal(17510,i[0].variation_id)
+    syn = Sample.find(21).sample_synonym
+    assert_equal('477',syn.name)
+  end
+  
+  def test_individual
+    n = Individual.count(:all)
+    assert_equal(10132,n)
+  end
+  
+  def test_individual_genotype_multiple_bp
+    n = IndividualGenotypeMultipleBp.count(:all)
+    assert_equal(712267,n)
+  end
+  
+  def test_compressed_genotype_single_bp
+    n = CompressedGenotypeSingleBp.count(:all)
+    assert_equal(12736658,n)
+  end
+  
+  def test_read_coverage
+    n = ReadCoverage.count(:all)
+    assert_equal(6521608,n)
+  end
+  
+  def test_population
+    n = Population.count(:all)
+    assert_equal(7690,n)
+  end
+  
+  def test_variation
+    n = Variation.count(:all)
+    assert_equal(18909925,n)
+    
+    syn = Variation.find(712422).variation_synonyms
+    assert_equal(6,syn.size)
+    assert_equal('SNP_A-1507972',syn[0].name)
+    
+    flanking = Variation.find(10000).flanking_sequence
+    assert_equal(3705521,flanking.up_seq_region_start)
+    assert_equal(3705770,flanking.up_seq_region_end)
+    assert_equal(3705772,flanking.down_seq_region_start)
+    assert_equal(3706021,flanking.down_seq_region_end)
+    assert_equal(27509,flanking.seq_region_id)
+    assert_equal(1,flanking.seq_region_strand)
+    
+    ag = Variation.find(10000).allele_groups
+    assert_nil ag[0]
+    
+    pg = Variation.find(10000).population_genotypes
+    assert_equal(12,pg.size)
+    assert_equal('C',pg[0].allele_1)
+    assert_equal('C',pg[0].allele_2)
+    assert_equal(1,pg[0].frequency)
+    
+    a = Variation.find(115).alleles
+    assert_equal(8,a.size)
+    assert_equal('C',a[0].allele)
+    assert_equal(0.733,a[0].frequency)
+    
+    vf = Variation.find(5345540).variation_features[0]
+    assert_equal('T/A',vf.allele_string)
+    assert_equal('rs8189747',vf.variation_name)
+    assert_equal(27526,vf.seq_region_id)
+    assert_equal(24606076,vf.seq_region_start)
+    assert_equal(24606076,vf.seq_region_end)
+    assert_equal(1,vf.seq_region_strand)
+    
+    vg = Variation.find(1352735).variation_groups
+    assert_nil vg[0]
+    
+    i = Variation.find(1533176).individual_genotype_multiple_bps
+    assert_equal(42,i.size)
+  end
+  
+  def test_variation_feature
+    vf_sample = VariationFeature.find(38461).samples
+    assert_equal(8,vf_sample.size)
+    assert_equal('PERLEGEN:AFD_EUR_PANEL',vf_sample[0].name)
+  end
+  
+  def test_variation_transcript
+    t = Variation.find_by_name('rs7671997').variation_features[0].transcript_variations
+    assert_equal(2,t.size)
+    transcript = t[0].transcript
+    assert_equal('protein_coding',transcript.biotype)
+    assert_equal(2230096,transcript.seq_region_start)
+    assert_equal(2243860,transcript.seq_region_end)
+    assert_equal('ENST00000243706',transcript.stable_id)
+    e = transcript.exons
+    assert_equal('CTCCCGTGAGGCAGTGCGAGGCGCGCGGGGCACGGAGGGCGGTGGCGGCGGGCTCCTGCGAGAAGCAAGCGGAACTTCCTGAG',e[0].seq.upcase)
+  end
+  
+  def test_source
+    syn = Source.find(1).sample_synonyms
+    assert_equal(17806,syn.size)
+    
+    ag = Source.find(1).allele_groups
+    assert_nil ag[0]
+  end
+end

data/test/unit/release_56/variation/test_variation.rb

@@ -0,0 +1,68 @@
+#
+# = test/unit/release_50/variation/test_variation.tb - Unit test for Ensembl::Variation
+#
+# Copyright::   Copyright (C) 2009
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+# License::     Ruby's
+#
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'lib/ensembl'
+
+include Ensembl::Variation
+
+class TestVariation < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.connect('homo_sapiens',56)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_fetch_region
+    vf = Variation.find_by_name('rs2076175').variation_features[0]
+    slice = vf.fetch_region
+    assert_equal(29708370,slice.start)
+    assert_equal(29718370,slice.stop)
+    assert_equal('6',slice.seq_region.name)
+    slice = vf.fetch_region(30,30)
+    assert_equal(29713340,slice.start)
+    assert_equal(29713400,slice.stop)
+    assert_equal('CTCCCAGGACTGCTTCTGCCCACTGTCCCCGGGGCCCTGCCCTGCCTTTCTGCCTGTCACA',slice.seq.upcase)
+  end
+  
+  def test_flanking_seq
+    vf = Variation.find_by_name('rs2076175').variation_features[0]
+    up,down = vf.flanking_seq
+    assert_equal(29713371,up.start)
+    assert_equal(29713770,up.stop)
+    assert_equal(29712970,down.start)
+    assert_equal(29713369,down.stop)
+    assert_equal('GGGCCCTGCCCTGCCTTTCTGCCTGTCACAGAGCAGGAAGAGCTGACCATCCAGATGTCCCTCAGCGAGAAACCCTGACTGCACAGATCCATCCTGGGACAGCACCGTGAGGTTGTAACAAAGACTGTGGGGCTCTGGGGAAGAGGAAATCACAGATGAAACTTCTTCCTGGAAGTAACTTCACATCAATGTTTAACACACAGGTCTGCTGTCCCGACCTTCCTGAGGAGGCAGGAAATGCACACGGGCAAAGGGACAAGAATGAGGATTTCAGACGCAAGGAAAACTGGGAAGGTGGGAGGATAGAGGAGGGGACTGAGGAACAGAAGAAGGGGGAATGGGGATGGCAAACTTGTAGGCCAGGTGCCAGGGCAGGGCAGCCACAGGCCCCCTCAGGATA',
+                  up.seq.upcase)
+    assert_equal('TCCTGATCTCACAAACCCTAATCTCCTGGAGGGAATGCAAGGCTGCCTGCCCCTACCCAGCAGTGACTTCTCCATTCCAGTCCAAGTGAGGAACTCGGACCAGGAAGGACCCCTCCCTGGCCCTCTTCCATCCCTCCCTGTGTGGGCTGAGCCCCGCTGAGCACCATTCCTCACCCCTACTCACAGCCAAATCCAGTGGGAAGAGACAGGTCCTGCTCTCTGCCCCCAACTCTCCTGGAAAAGGCCTCTCCCATTACTCTTGCCCACTGCCCACTCTCACCTCCTTTCTGGCCCTTGATATGAGCCAGGGTCCTCCTGAGCTCCTGCCCATTCTCTGTCAAGTCTTCAGTCTCTGTGTCCCAGGTCTCAGCTCCCAGGACTGCTTCTGCCCACTGTCCCC',
+                down.seq.upcase)
+                              
+  end
+  
+  def test_slice_variation
+    slice = Ensembl::Core::Slice.fetch_by_region('chromosome',1,100834,101331)
+    variations = slice.get_variation_features
+    assert_equal(6,variations.size)
+    
+    assert_equal('rs3912703',variations[0].variation_name)
+    assert_equal('ENSSNP5435782',variations[1].variation_name)
+    assert_equal('ENSSNP3491774',variations[2].variation_name)
+    assert_equal('ENSSNP283782',variations[3].variation_name)
+    assert_equal('ENSSNP4578340',variations[4].variation_name)
+
+  end
+  
+  
+  
+end

data/test/unit/test_connection.rb

@@ -0,0 +1,66 @@
+#
+# = test/unit/test_connection.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2009
+#               Jan Aerts <http://jandot.myopenid.com>
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+# License::     Ruby's
+#
+# $Id:
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+
+require 'ensembl'
+
+
+class TestConnection < Test::Unit::TestCase
+
+  def test_remote_core_connection
+    assert_nothing_raised do 
+      Ensembl::Core::DBConnection.connect('homo_sapiens',56)
+    end
+  end
+
+  # This is to check if the overwrite of the default parameters is possible, 
+  # so you can specify an Ensembl database on a host that is different from the official Ensembl website.
+
+  def test_local_core_connection
+    
+    # Change username, password, host and port in order to test the connection with a different Ensembl db server
+    assert_nothing_raised do 
+      Ensembl::Core::DBConnection.connect('homo_sapiens',56,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 5306)
+    end
+  end
+  
+  def test_remote_variation_connection
+    assert_nothing_raised do 
+      Ensembl::Variation::DBConnection.connect('homo_sapiens',56)
+    end
+  end
+  
+  def test_local_variation_connection
+    
+    # Change username, password, host and port in order to test the connection with a different Ensembl db server
+    assert_nothing_raised do 
+      Ensembl::Variation::DBConnection.connect('bos_taurus',56,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 5306)
+    end
+  end
+  
+  def test_connection_ensembl_genomes
+    assert_nothing_raised do 
+      Ensembl::Core::DBConnection.ensemblgenomes_connect('Staphylococcus_aureus_MRSA252',3)
+    end
+  end
+  
+  def test_manual_connection_ensembl_genomes
+    assert_nothing_raised do
+      Ensembl::Core::DBConnection.connect("bacillus_collection",3,:host => "mysql.ebi.ac.uk", :port => 4157)
+    end
+  end
+  
+end
+

data/test/unit/test_releases.rb

@@ -0,0 +1,136 @@
+#
+# = test/unit/test_releases.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2009
+#               Jan Aerts <http://jandot.myopenid.com>
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+# License::     Ruby's
+#
+# $Id:
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+
+require 'lib/ensembl'
+
+include Ensembl::Core
+
+class TestRelease53 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_gene_stable_id_human
+    DBConnection.connect('homo_sapiens', 53)
+    @slice = Slice.fetch_by_region('chromosome','1',1000,100000)
+    assert_equal(["ENSG00000146556","ENSG00000177693","ENSG00000197490","ENSG00000205292","ENSG00000219789","ENSG00000221311","ENSG00000222003","ENSG00000222027"], @slice.genes.collect{|g| g.stable_id}.sort)
+  end
+end
+
+class TestRelease50 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+
+  def test_gene_stable_id
+    DBConnection.connect('homo_sapiens', 50)
+    @slice = Slice.fetch_by_region('chromosome','1',1000,100000)
+    assert_equal(["ENSG00000146556", "ENSG00000177693", "ENSG00000197194", "ENSG00000197490", "ENSG00000205292", "ENSG00000219789", "ENSG00000221311"], @slice.genes.collect{|g| g.stable_id}.sort)
+  end
+end
+
+class TestRelease49 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_slice_and_genes_mouse
+    DBConnection.connect('mus_musculus',49)
+    
+    slice = Slice.fetch_by_region('chromosome',"19",52571924,52572023)
+    assert_equal("AAGGTTGTATTCTAGTTTGCTCTCTGTTATTGTGACAAAGACAGGACCAAAGAAACTTGAGTAGGAAATGGTTGATAAAATCTTACAAGTTAGAAGGCAG",slice.seq.upcase)
+    
+    gene = Gene.find_by_stable_id("ENSMUSG00000017167")
+    assert_equal(101037431, gene.start)
+    assert_equal(101052034, gene.stop)
+    assert_equal(1,gene.transcripts.size)
+    assert_equal("ENSMUST00000103109",gene.transcripts[0].stable_id)
+  end
+  
+end
+
+class TestRelease47 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_slice_and_genes_mouse
+    DBConnection.connect('mus_musculus',47)
+    
+    slice = Slice.fetch_by_region('chromosome',"5",123840876,123912619)
+    genes = slice.genes
+    assert_equal("ENSMUSG00000038342",genes[0].stable_id)
+    slice = Slice.fetch_by_region('chromosome',"5",123840876,123840975)
+    assert_equal("TCTCAGTTCAGGTTCTATGGGGGGGAGGGGAGGGAATGAAAAGGATGTTAACAATCACCATCACCAGGGGGGACCAATTTGAAGATCTGATCGCCGGTGT",slice.seq.upcase)
+    
+    gene = Gene.find_by_stable_id("ENSMUSG00000017167")
+    assert_equal(101037431, gene.start)
+    assert_equal(101052034, gene.stop)
+    assert_equal(1,gene.transcripts.size)
+    assert_equal("ENSMUST00000103109",gene.transcripts[0].stable_id)
+  end
+  
+end
+
+class TestRelease45 < Test::Unit::TestCase
+
+  def teardown
+    DBConnection.remove_connection
+  end
+
+  def test_gene_stable_id_human
+    DBConnection.connect('homo_sapiens', 45)
+    @slice = Slice.fetch_by_region('chromosome','1',1000,100000)
+    assert_equal(["ENSG00000146556", "ENSG00000177693", "ENSG00000197194", "ENSG00000197490", "ENSG00000205292"], @slice.genes.collect{|g| g.stable_id}.sort)
+  end
+  
+  def test_slice_and_genes_mouse
+    DBConnection.connect('mus_musculus',45)
+    
+    slice = Slice.fetch_by_region('chromosome',"11",101037431,101037530)
+    assert_equal("ACTCTATCCAACTGAAACTGGAGATTAGTAACAGGGAAAAACAAACTCAACTGACAGCTGCTCCCAGTACAGTTCTTATGGTACAGGGAGCGTGGGAGTG",slice.seq.upcase)
+    
+    gene = Gene.find_by_stable_id("ENSMUSG00000017167")
+    assert_equal(100992131,gene.start)
+    assert_equal(101006814,gene.stop)
+    assert_equal("11",gene.seq_region.name)
+    assert_equal(2,gene.transcripts.size)
+  end
+  
+end
+ 
+class TestRelease37 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+
+  def test_gene_stable_id_human
+    DBConnection.connect('homo_sapiens', 37)
+    @slice = Slice.fetch_by_region('chromosome','1',1000,100000)
+    assert_equal(["ENSG00000146556", "ENSG00000177693", "ENSG00000197194", "ENSG00000197490"], @slice.genes.collect{|g| g.stable_id}.sort)
+  end
+end
+ 
+
+
+
+
+