bio-ensembl 1.1.0

data/test/release_50/core/test_transform.rb

@@ -0,0 +1,217 @@
+#
+# = test/unit/test_transform.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2007
+#               Jan Aerts <http://jandot.myopenid.com>
+# License::     Ruby's
+#
+# $Id:
+require File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+include Ensembl::Core
+DBConnection.connect('bos_taurus', 50)
+
+# 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
+  # |-------|========>-------------------------> chromosome
+  #         ^        ^
+  #         |        |
+  # |-------|========>-------------------------> chromosome
+  # This should return itself.
+  def test_fw
+    source_gene = Gene.find(6043)
+    target_gene = source_gene.transform('chromosome')
+
+    assert_equal('4', source_gene.seq_region.name)
+    assert_equal(4595538, source_gene.seq_region_start)
+    assert_equal(4827723, source_gene.seq_region_end)
+    assert_equal(1, source_gene.seq_region_strand)
+    assert_equal('4', target_gene.seq_region.name)
+    assert_equal(4595538, target_gene.seq_region_start)
+    assert_equal(4827723, target_gene.seq_region_end)
+    assert_equal(1, target_gene.seq_region_strand)
+  end
+
+  # |-------<========|-------------------------> chromosome
+  #         ^        ^
+  #         |        |
+  # |-------<========|-------------------------> chromosome
+  # This should return itself.
+  def test_rev
+    source_gene = Gene.find(6053)
+    target_gene = source_gene.transform('chromosome')
+
+    assert_equal('4', source_gene.seq_region.name)
+    assert_equal(5199677, source_gene.seq_region_start)
+    assert_equal(5201728, source_gene.seq_region_end)
+    assert_equal(-1, source_gene.seq_region_strand)
+    assert_equal('4', target_gene.seq_region.name)
+    assert_equal(5199677, target_gene.seq_region_start)
+    assert_equal(5201728, target_gene.seq_region_end)
+    assert_equal(-1, target_gene.seq_region_strand)
+  end
+end
+
+## Test names refer to:
+## (1) direction of gene vs chromosome
+## (2) direction of component (scaffold) vs assembly (chromosome)
+#class TransformFromComponentToAssembly < Test::Unit::TestCase
+#  def test_fw_fw
+#    assert true
+#  end
+#
+#  def test_fw_rev
+#    assert true
+#  end
+#
+#  def test_rev_fw
+#    assert true
+#  end
+#
+#  def test_rev_rev
+#    assert true
+#  end
+#end
+#
+## Test names refer to:
+## (1) direction of gene vs chromosome
+## (2) direction of component (scaffold) vs assembly (chromosome)
+## We have to test for features that are covered by a scaffold, and those
+## overlapping more than 1 scaffold.
+#class TransformFromAssemblyToComponent < Test::Unit::TestCase
+#  #       |-----------------> scaffold
+#  #           ^     ^
+#  #           |     |
+#  # |---------|=====>-----------------------------> chromosome
+#  def test_fw_fw_full_overlap
+#    source_gene = Gene.find(2995)
+#    target_gene = source_gene.transform('scaffold')
+#
+#    assert_equal('4', source_gene.seq_region.name)
+#    assert_equal(10333321, source_gene.seq_region_start)
+#    assert_equal(10510842, source_gene.seq_region_end)
+#    assert_equal(1, source_gene.seq_region_strand)
+#    assert_equal('Chr4.003.12', target_gene.seq_region.name)
+#    assert_equal(43842, target_gene.seq_region_start)
+#    assert_equal(221363, target_gene.seq_region_end)
+#    assert_equal(1, target_gene.seq_region_strand)
+#  end
+#
+#  #       |-----------------> scaffold
+#  #       |
+#  #       |
+#  # |---|===>-------------------------------> chromosome
+#  def test_fw_fw_partial_overlap
+#    source_feature = PredictionTranscript.find(52425)
+#    target_feature = source_feature.transform('scaffold')
+#
+#    assert_equal('4', source_feature.seq_region.name)
+#    assert_equal(1443280, source_feature.seq_region_start)
+#    assert_equal(1482777, source_feature.seq_region_end)
+#    assert_equal(1, source_feature.seq_region_strand)
+#    assert_equal(nil, target_feature)
+#  end
+#
+#  #       <-----------------| scaffold
+#  #            ^     ^
+#  #            |     |
+#  # |----------|=====>-----------------------------> chromosome
+#  def test_fw_rev_full_overlap
+#    source_gene = Gene.find(2708)
+#    target_gene = source_gene.transform('scaffold')
+#
+#    assert_equal('4', source_gene.seq_region.name)
+#    assert_equal(8312492, source_gene.seq_region_start)
+#    assert_equal(8312812, source_gene.seq_region_end)
+#    assert_equal(1, source_gene.seq_region_strand)
+#    assert_equal('Chr4.003.10', target_gene.seq_region.name)
+#    assert_equal(1774466, target_gene.seq_region_start)
+#    assert_equal(1774786, target_gene.seq_region_end)
+#    assert_equal(-1, target_gene.seq_region_strand)
+#  end
+#
+#  #       <-----------------| scaffold
+#  #                         |
+#  #                         |
+#  # |---------------------|===>------------------> chromosome
+#  def test_fw_rev_partial_overlap
+#    source_feature = PredictionTranscript.find(23305)
+#    target_feature = source_feature.transform('scaffold')
+#
+#    assert_equal('4', source_feature.seq_region.name)
+#    assert_equal(10008188, source_feature.seq_region_start)
+#    assert_equal(10156104, source_feature.seq_region_end)
+#    assert_equal(1, source_feature.seq_region_strand)
+#    assert_equal(nil, target_feature)
+#  end
+#
+#  #       |-----------------> scaffold
+#  #       |    ^     ^
+#  #       |    |     |
+#  # |---<===|--<=====|-----------------------------> chromosome
+#  def test_rev_fw_full_overlap
+#    source_gene = Gene.find(3124)
+#    target_gene = source_gene.transform('scaffold')
+#
+#    assert_equal('4', source_gene.seq_region.name)
+#    assert_equal(10353230, source_gene.seq_region_start)
+#    assert_equal(10371155, source_gene.seq_region_end)
+#    assert_equal(-1, source_gene.seq_region_strand)
+#    assert_equal('Chr4.003.12', target_gene.seq_region.name)
+#    assert_equal(63751, target_gene.seq_region_start)
+#    assert_equal(81676, target_gene.seq_region_end)
+#    assert_equal(-1, target_gene.seq_region_strand)
+#  end
+#
+#  #       |-----------------> scaffold
+#  #                         |
+#  #                         |
+#  # |---------------------<===|------------------> chromosome
+#  def test_rev_fw_partial_overlap
+#    source_feature = PredictionTranscript.find(24185)
+#    target_feature = source_feature.transform('scaffold')
+#
+#    assert_equal('4', source_feature.seq_region.name)
+#    assert_equal(11389212, source_feature.seq_region_start)
+#    assert_equal(11471635, source_feature.seq_region_end)
+#    assert_equal(-1, source_feature.seq_region_strand)
+#    assert_equal(nil, target_feature)
+#  end
+#
+#  #       <-----------------| scaffold
+#  #       |    ^     ^
+#  #       |    |     |
+#  # |---<===|--<=====|-----------------------------> chromosome
+#  def test_rev_rev_full_overlap
+#    source_gene = Gene.find(2408)
+#    target_gene = source_gene.transform('scaffold')
+#
+#    assert_equal('4', source_gene.seq_region.name)
+#    assert_equal(8104409, source_gene.seq_region_start)
+#    assert_equal(8496477, source_gene.seq_region_end)
+#    assert_equal(-1, source_gene.seq_region_strand)
+#    assert_equal('Chr4.003.10', target_gene.seq_region.name)
+#    assert_equal(1590801, target_gene.seq_region_start)
+#    assert_equal(1982869, target_gene.seq_region_end)
+#    assert_equal(1, target_gene.seq_region_strand)
+#  end
+#
+#  #       <-----------------| scaffold
+#  #       |
+#  #       |
+#  # |---<===|-----------------------------> chromosome
+#  def test_rev_rev_partial_overlap
+#    source_feature = Transcript.find(14723)
+#    target_feature = source_feature.transform('scaffold')
+#
+#    assert_equal('4', source_feature.seq_region.name)
+#    assert_equal(55713316, source_feature.seq_region_start)
+#    assert_equal(55792273, source_feature.seq_region_end)
+#    assert_equal(-1, source_feature.seq_region_strand)
+#    assert_equal(nil, target_feature)
+#  end
+#
+#end

data/test/release_50/variation/test_activerecord.rb

@@ -0,0 +1,138 @@
+#
+# = test/unit/release_50/variation/test_activerecord.rb - Unit test for Ensembl::Variation
+#
+# Copyright::   Copyright (C) 2008 Francesco Strozzi <francesco.strozzi@gmail.com>
+#
+# License::     Ruby's
+#
+# $Id:
+require File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+include Ensembl::Variation
+DBConnection.connect('homo_sapiens',50)
+
+class ActiveRecordVariation < Test::Unit::TestCase
+  
+  def test_allele
+    allele = Allele.find(1)
+    assert_equal('T', allele.allele)
+    assert_equal(0.04, allele.frequency)
+  end
+  
+  def test_allele_group
+    n = AlleleGroup.count(:all)
+    assert_equal(0, n)
+  end
+
+  def test_sample
+    n = Sample.count(:all)
+    assert_equal(12385,n)
+    individual = Sample.find(5499).individual
+    assert_equal('Male',individual.gender)
+    i = Sample.find(6201).individual_genotype_multiple_bp
+    assert_equal(1256,i.size)
+    assert_equal(548383,i[0].variation_id)
+    syn = Sample.find(17).sample_synonym
+    assert_equal('5',syn.name)
+  end
+  
+  def test_individual
+    n = Individual.count(:all)
+    assert_equal(7769,n)
+  end
+  
+  def test_individual_genotype_multiple_bp
+    n = IndividualGenotypeMultipleBp.count(:all)
+    assert_equal(835033,n)
+  end
+  
+  def test_compressed_genotype_single_bp
+    n = CompressedGenotypeSingleBp.count(:all)
+    assert_equal(12473477,n)
+  end
+  
+  def test_read_coverage
+    n = ReadCoverage.count(:all)
+    assert_equal(9328349,n)
+  end
+  
+  def test_population
+    n = Population.count(:all)
+    assert_equal(4616,n)
+  end
+  
+  def test_variation
+    n = Variation.count(:all)
+    assert_equal(13383219,n)
+    
+    syn = Variation.find(27).variation_synonyms
+    assert_equal('SNP001745772',syn[0].name)
+    
+    flanking = Variation.find(130).flanking_sequence
+    assert_equal(24910767,flanking.up_seq_region_start)
+    assert_equal(24911281,flanking.up_seq_region_end)
+    assert_equal(24911283,flanking.down_seq_region_start)
+    assert_equal(24911367,flanking.down_seq_region_end)
+    assert_equal(226030,flanking.seq_region_id)
+    assert_equal(1,flanking.seq_region_strand)
+    
+    ag = Variation.find(130).allele_groups
+    assert_nil ag[0]
+    
+    pg = Variation.find(1125).population_genotypes
+    assert_equal(26,pg.size)
+    assert_equal('A',pg[0].allele_1)
+    assert_equal('A',pg[0].allele_2)
+    assert_equal(0.2,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('G/A',vf.allele_string)
+    assert_equal('rs8175337',vf.variation_name)
+    assert_equal(226028,vf.seq_region_id)
+    assert_equal(10052344,vf.seq_region_start)
+    assert_equal(10052344,vf.seq_region_end)
+    assert_equal(1,vf.seq_region_strand)
+    
+    vg = Variation.find(1352735).variation_groups
+    assert_nil vg[0]
+    
+    i = Variation.find(1352735).individual_genotype_multiple_bps
+    assert_equal(31,i.size)
+  end
+  
+  def test_variation_feature
+    vf_sample = VariationFeature.find(4571).samples
+    assert_equal(5,vf_sample.size)
+    assert_equal('PERLEGEN:AFD_EUR_PANEL',vf_sample[0].name)
+  end
+  
+  def test_variation_transcript
+    t = Variation.find_by_name('rs35303525').variation_features[0].transcript_variations
+    assert_equal(5,t.size)
+    assert_equal(69644,t[0].transcript_id)
+    transcript = t[0].transcript
+    assert_equal('protein_coding',transcript.biotype) 
+    assert_equal(2050017,transcript.seq_region_start)
+    assert_equal(2148813,transcript.seq_region_end)
+    assert_equal('ENST00000382857',transcript.stable_id)
+    e = transcript.exons
+    assert_equal('ATGGCTGTGGGGAGCCAG',e[0].seq.upcase)
+  end
+  
+  def test_source
+    syn = Source.find(1).sample_synonyms
+    assert_equal('2',syn[0].name)
+    
+    ag = Source.find(1).allele_groups
+    assert_nil ag[0]
+    
+    v = Source.find(6).variations
+    assert_equal(19,v.size)
+    assert_equal('SNP_A-8319323',v[0].name)
+  end
+end

data/test/release_50/variation/test_variation.rb

@@ -0,0 +1,79 @@
+#
+# = test/unit/release_50/variation/test_variation.tb - Unit test for Ensembl::Variation
+#
+# Copyright::   Copyright (C) 2008 Francesco Strozzi <francesco.strozzi@gmail.com>
+#
+# License::     Ruby's
+#
+require File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+include Ensembl::Variation
+
+DBConnection.connect('homo_sapiens',50)
+
+class TestVariation < Test::Unit::TestCase
+  
+  def test_fetch_region
+    vf = Variation.find_by_name('rs2076175').variation_features[0]
+    slice = vf.fetch_region
+    assert_equal(29816349,slice.start)
+    assert_equal(29826349,slice.stop)
+    assert_equal('6',slice.seq_region.name)
+    slice = vf.fetch_region(30,30)
+    assert_equal(29821319,slice.start)
+    assert_equal(29821379,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(29820949,up.start)
+    assert_equal(29821348,up.stop)
+    assert_equal(29821350,down.start)
+    assert_equal(29821749,down.stop)
+    assert_equal('TCCTGATCTCACAAACCCTAATCTCCTGGAGGGAATGCAAGGCTGCCTGCCCCTACCCAGCAGTGACTTCTCCATTCCAGTCCAAGTGAGGAACTCGGACCAGGAAGGACCCCTCCCTGGCCCTCTTCCATCCCTCCCTGTGTGGGCTGAGCCCCGCTGAGCACCATTCCTCACCCCTACTCACAGCCAAATCCAGTGGGAAGAGACAGGTCCTGCTCTCTGCCCCCAACTCTCCTGGAAAAGGCCTCTCCCATTACTCTTGCCCACTGCCCACTCTCACCTCCTTTCTGGCCCTTGATATGAGCCAGGGTCCTCCTGAGCTCCTGCCCATTCTCTGTCAAGTCTTCAGTCTCTGTGTCCCAGGTCTCAGCTCCCAGGACTGCTTCTGCCCACTGTCCCC',
+                  up.seq.upcase)
+    assert_equal('GGGCCCTGCCCTGCCTTTCTGCCTGTCACAGAGCAGGAAGAGCTGACCATCCAGATGTCCCTCAGCGAGAAACCCTGACTGCACAGATCCATCCTGGGACAGCACCGTGAGGTTGTAACAAAGACTGTGGGGCTCTGGGGAAGAGGAAATCACAGATGAAACTTCTTCCTGGAAGTAACTTCACATCAATGTTTAACACACAGGTCTGCTGTCCCGACCTTCCTGAGGAGGCAGGAAATGCACACGGGCAAAGGGACAAGAATGAGGATTTCAGACGCAAGGAAAACTGGGAAGGTGGGAGGATAGAGGAGGGGACTGAGGAACAGAAGAAGGGGGAATGGGGATGGCAAACTTGTAGGCCAGGTGCCAGGGCAGGGCAGCCACAGGCCCCCTCAGGATA',
+                down.seq.upcase)
+                              
+  end
+  
+  def test_slice_variation
+    slice = Ensembl::Core::Slice.fetch_by_region('chromosome',1,50000,51000)
+    variations = slice.get_variation_features
+    assert_equal(9,variations.size)
+    assert_equal('ENSSNP4691381',variations[0].variation_name)
+    assert_equal('ENSSNP9996411',variations[1].variation_name)
+    assert_equal('rs2691281',variations[2].variation_name)
+    assert_equal('ENSSNP4068519',variations[3].variation_name)
+    assert_equal('ENSSNP230814',variations[4].variation_name)
+    assert_equal('ENSSNP4010737',variations[5].variation_name)
+    assert_equal('rs2531295',variations[6].variation_name)
+    assert_equal('ENSSNP5092147',variations[7].variation_name)
+    assert_equal('ENSSNP5346602',variations[8].variation_name)
+    
+    genotyped = slice.get_genotyped_variation_features
+    assert_equal(7,genotyped.size)
+    assert_equal('ENSSNP4691381',genotyped[0].variation_name)
+    assert_equal('genotyped',genotyped[0].flags)
+    assert_equal('ENSSNP9996411',genotyped[1].variation_name)
+    assert_equal('genotyped',genotyped[1].flags)
+    assert_equal('ENSSNP4068519',genotyped[2].variation_name)
+    assert_equal('genotyped',genotyped[2].flags)
+    assert_equal('ENSSNP230814',genotyped[3].variation_name)
+    assert_equal('genotyped',genotyped[3].flags)
+    assert_equal('ENSSNP4010737',genotyped[4].variation_name)
+    assert_equal('genotyped',genotyped[4].flags)
+    assert_equal('ENSSNP5092147',genotyped[5].variation_name)
+    assert_equal('genotyped',genotyped[5].flags)
+    assert_equal('ENSSNP5346602',genotyped[6].variation_name)
+    assert_equal('genotyped',genotyped[6].flags)
+    
+    v = variations[0].variation
+    assert_equal(16366812,v.variation_id)
+  end
+  
+  
+  
+end

data/test/release_53/core/test_gene.rb

@@ -0,0 +1,61 @@
+#
+# = test/unit/release_53/core/test_gene.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2009 Francesco Strozzi <francesco.strozzi@gmail.com>
+#
+# License::     Ruby's
+#
+# $Id:
+
+require File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+include Ensembl::Core
+
+class TestGene < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.connect('homo_sapiens', 53)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_gene
+    g = Gene.find_by_stable_id("ENSG00000006451")
+    assert_equal("ENSG00000006451",g.stable_id)
+    assert_equal("7",g.seq_region.name)
+    assert_equal(39629687,g.start)
+    assert_equal(39714240,g.stop)
+    assert_equal(1,g.strand)
+    assert_equal(84554,g.seq.length)
+    assert_equal("Ras-related protein Ral-A Precursor  [Source:UniProtKB/Swiss-Prot;Acc:P11233]",g.description)
+    assert_equal("RALA",g.name)
+  end
+  
+  def test_transcript
+    g = Gene.find_by_stable_id("ENSG00000006451")
+    t = g.transcripts
+    assert_equal(1,t.size)
+    assert_equal("ENST00000005257",t[0].stable_id)
+    t = t[0]
+    assert_equal(2792,t.seq.length)
+  end
+  
+  def test_exons
+    t = Transcript.find_by_stable_id("ENST00000005257")
+    e = t.exons
+    assert_equal(5,e.size)
+    assert_equal("ENSE00001324495",e[0].stable_id)
+    seq1 = "AAGTGATCTGTGGCGGCTGCTGCAGAGCCGCCAGGAGGAGGGTGGATCTCCCCAGAGCAAAGCGTCGGAGTCCTCCTCCTCCTTCTCCTCCTCCTCCTCCTCCTCCTCCAGCCGCCCAGGCTCCCCCGCCACCCGTCAGACTCCTCCTTCGACCGCTCCCGGCGCGGGGCCTTCCAGGCGACAAGGACCGAGTACCCTCCGGCCGGAGCCACGCAGCCGCGGCTTCCGGAGCCCTCGGGGCGGCGGACTGGCTCGCGGTGCAG"
+    assert_equal(seq1,e[0].seq.upcase)
+    assert_equal(39629687,e[0].start)
+    assert_equal(39629949,e[0].stop)
+    assert_equal("ENSE00000832451",e[1].stable_id)
+    seq2 = "ATTCTTCTTAATCCTTTGGTGAAAACTGAGACACAAAATGGCTGCAAATAAGCCCAAGGGTCAGAATTCTTTGGCTTTACACAAAGTCATCATGGTGGGCAGTGGTGGCGTGGGCAAGTCAGCTCTGACTCTACAGTTCATGTACGATGAG"
+    assert_equal(seq2,e[1].seq.upcase)
+    assert_equal(39692755,e[1].start)
+    assert_equal(39692905,e[1].stop)
+  end
+
+end