bio-ensembl 1.1.0

data/test/release_56/core/test_gene.rb

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+#
+# = test/unit/release_56/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', 56)
+  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(39663082,g.start)
+    assert_equal(39747723 ,g.stop)
+    assert_equal(1,g.strand)
+    assert_equal(84642,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(5,t.size)
+    assert_equal("ENST00000434466",t[0].stable_id)
+    t = t[0]
+    assert_equal(768,t.seq.length)
+  end
+  
+  def test_exons
+    t = Transcript.find_by_stable_id("ENST00000005257")
+    e = t.exons
+    assert_equal(5,e.size)
+    assert_equal("ENSE00001829077",e[0].stable_id)
+    seq1 = "AGGCCCATGATCACCCTCCTCTCAGCCCACGGACAGGAAGTCGCTCCCCAGCTGCCCCGCCCCGCTCCCCAGCGCCCCGGAAGTGATCTGTGGCGGCTGCTGCAGAGCCGCCAGGAGGAGGGTGGATCTCCCCAGAGCAAAGCGTCGGAGTCCTCCTCCTCCTTCTCCTCCTCCTCCTCCTCCTCCTCCAGCCGCCCAGGCTCCCCCGCCACCCGTCAGACTCCTCCTTCGACCGCTCCCGGCGCGGGGCCTTCCAGGCGACAAGGACCGAGTACCCTCCGGCCGGAGCCACGCAGCCGCGGCTTCCGGAGCCCTCGGGGCGGCGGACTGGCTCGCGGTGCAG"
+    assert_equal(seq1,e[0].seq.upcase)
+    assert_equal(39663082,e[0].start)
+    assert_equal(39663424,e[0].stop)
+    assert_equal("ENSE00000832451",e[1].stable_id)
+    seq2 = "ATTCTTCTTAATCCTTTGGTGAAAACTGAGACACAAAATGGCTGCAAATAAGCCCAAGGGTCAGAATTCTTTGGCTTTACACAAAGTCATCATGGTGGGCAGTGGTGGCGTGGGCAAGTCAGCTCTGACTCTACAGTTCATGTACGATGAG"
+    assert_equal(seq2,e[1].seq.upcase)
+    assert_equal(39726230,e[1].start)
+    assert_equal(39726380,e[1].stop)
+  end
+
+end

data/test/release_56/core/test_project.rb

@@ -0,0 +1,91 @@
+#
+# = test/unit/release_53/core/test_project.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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+include Ensembl::Core
+
+class SliceProjectFromAssemblyToComponentForwardStrands < Test::Unit::TestCase
+  def setup
+    DBConnection.connect('bos_taurus', 56)
+    @source_slice_single_contig = Slice.fetch_by_region('chromosome', '20', 175000, 180000)
+    @target_slices_single_contig = @source_slice_single_contig.project('contig')
+
+    @source_slice_two_contigs = Slice.fetch_by_region('chromosome','20', 175000, 190000)
+    @target_slices_two_contigs = @source_slice_two_contigs.project('contig')
+
+    @source_slice_contigs_with_strand = Slice.fetch_by_region('chromosome', '20', 160000, 190000)
+    @target_slices_contigs_with_strand = @source_slice_contigs_with_strand.project('contig')
+
+    @source_slice_contigs_with_strand_ends_in_gaps = Slice.fetch_by_region('chromosome', '20', 170950, 196000)
+    @target_slices_contigs_with_strand_ends_in_gaps = @source_slice_contigs_with_strand_ends_in_gaps.project('contig')
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+
+  #     |-----------------> contig
+  #         ^          ^
+  #         |          |
+  # |------------------------------------------> chromosome
+  def test_project_from_assembly_to_single_component
+    # Position 175000 on chr20 is position 4030 on contig, position 180000 is 9030
+    assert_equal('AAFC03028970', @target_slices_single_contig[0].seq_region.name)
+    assert_equal(4030, @target_slices_single_contig[0].start)
+    assert_equal(9030, @target_slices_single_contig[0].stop)
+  end
+
+  #     |----->   |--------> contig
+  #         ^          ^
+  #         |          |
+  # |------------------------------------------> chromosome
+  def test_project_from_assembly_to_two_components
+    # This chromosomal region is covered by contigs AAFC03028970, a gap and AAFC03028962
+    #  * Position 175000 on chr 20 is position 4030 on contig AAFC03028970
+    #  * Position 190000 on chr 20 is position 35 on contig AAFC03028962
+    assert_equal(3, @target_slices_two_contigs.length)
+    assert_equal('contig:Btau_4.0:AAFC03028970:4030:17365:1', @target_slices_two_contigs[0].display_name)
+    assert_equal(Gap, @target_slices_two_contigs[1].class)
+    assert_equal('contig:Btau_4.0:AAFC03028962:1:35:1', @target_slices_two_contigs[2].display_name)
+  end
+
+  #     |----->   <-------|   |------->  |------->  contig
+  #         ^                                 ^
+  #         |                                 |
+  # |--------------------------------------------------> chromosome
+  def test_project_from_assembly_to_contigs_with_strand
+    # This chromosomal region is covered by 4 contigs and 3 gaps
+    # One of the contigs are on the reverse strand.
+    assert_equal(7, @target_slices_contigs_with_strand.length)
+    assert_equal('contig:Btau_4.0:AAFC03028964:90:9214:1', @target_slices_contigs_with_strand[0].display_name)
+    assert_equal(Gap, @target_slices_contigs_with_strand[1].class)
+    assert_equal('contig:Btau_4.0:AAFC03028959:1:1746:-1', @target_slices_contigs_with_strand[2].display_name)
+    assert_equal(Gap, @target_slices_contigs_with_strand[3].class)
+    assert_equal('contig:Btau_4.0:AAFC03028970:1:17365:1', @target_slices_contigs_with_strand[4].display_name)
+    assert_equal(Gap, @target_slices_contigs_with_strand[5].class)
+    assert_equal('contig:Btau_4.0:AAFC03028962:1:35:1', @target_slices_contigs_with_strand[6].display_name)
+  end
+
+  #      <--|  |----->        contig
+  #   ^                 ^
+  #   |                 |
+  # |--------------------------------------------------> chromosome
+  def test_project_from_assembly_to_contigs_with_strand_and_ending_in_gaps
+    # This chromosomal region is covered by 2 contigs and 2 gaps at the end: GaCoGaCoGa
+    assert_equal(5, @target_slices_contigs_with_strand_ends_in_gaps.length)
+    assert_equal(Gap, @target_slices_contigs_with_strand_ends_in_gaps[0].class)
+    assert_equal('contig:Btau_4.0:AAFC03028970:1:17365:1', @target_slices_contigs_with_strand_ends_in_gaps[1].display_name)
+    assert_equal(Gap, @target_slices_contigs_with_strand_ends_in_gaps[2].class)
+    assert_equal('contig:Btau_4.0:AAFC03028962:1:5704:1', @target_slices_contigs_with_strand_ends_in_gaps[3].display_name)
+    assert_equal(Gap, @target_slices_contigs_with_strand_ends_in_gaps[4].class)
+  end
+  
+end

data/test/release_56/core/test_slice.rb

@@ -0,0 +1,49 @@
+#
+# = 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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+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/release_56/core/test_transform.rb

@@ -0,0 +1,57 @@
+#
+# = 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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+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/release_56/variation/test_activerecord.rb

@@ -0,0 +1,141 @@
+#
+# = test/unit/release_56/variation/test_activerecord.rb - Unit test for Ensembl::Variation
+#
+# 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::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)
+    assert_equal('INTRONIC',t[0].consequence_type)
+    assert_equal('5PRIME_UTR',t[1].consequence_type)
+    assert_equal(15008544,t[0].variation_feature_id)
+    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/release_56/variation/test_consequence.rb

@@ -0,0 +1,131 @@
+#
+# = test/unit/release_56/variation/test_variation.tb - Unit test for Ensembl::Variation
+#
+# Copyright::   Copyright (C) 2009
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+# License::     Ruby's
+#
+require File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+include Ensembl::Variation
+
+class TestVariation < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.connect('homo_sapiens',56)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_calculations
+    
+  # INTERGENIC
+    vf = VariationFeature.new(:seq_region_id => SeqRegion.find_by_name("X").seq_region_id, :seq_region_start => 23694, :seq_region_end => 23694, :seq_region_strand => 1, :allele_string => "A/T",:variation_name => "fake_SNP")
+    tv = vf.transcript_variations
+    assert_instance_of(TranscriptVariation,tv[0])
+    assert_equal("INTERGENIC",tv[0].consequence_type)
+
+  
+  # 3PRIME_UTR
+    vf = VariationFeature.new(:seq_region_id => 27506, :seq_region_start => 96810688, :seq_region_end => 96810688, :seq_region_strand => 1, :allele_string => "G/C", :variation_name => "rs16869283")
+    tv = vf.transcript_variations
+    assert_equal("3PRIME_UTR", tv[1].consequence_type) 
+  
+  # 5PRIME_UTR
+    vf = VariationFeature.new(:seq_region_id => 27506, :seq_region_start => 158536411, :seq_region_end => 158536411, :seq_region_strand => 1, :allele_string => "T/C", :variation_name => "rs71547565")
+    tv = vf.transcript_variations
+    assert_equal("5PRIME_UTR", tv[3].consequence_type) 
+  
+  # UPSTREAM
+    vf = VariationFeature.new(:seq_region_id => 27506, :seq_region_start => 96831018, :seq_region_end => 96831018, :seq_region_strand => 1, :allele_string => "G/T", :variation_name => "rs6975185")
+    tv = vf.transcript_variations
+    assert_equal("UPSTREAM",tv[0].consequence_type)
+  
+  # DOWNSTREAM  
+    vf = VariationFeature.new(:seq_region_id => 27506, :seq_region_start => 105727321, :seq_region_end => 105727321, :seq_region_strand => 1, :allele_string => "G/T", :variation_name => "rs35113830")
+    tv = vf.transcript_variations
+    assert_equal("DOWNSTREAM",tv[0].consequence_type)
+  
+  # WITHIN_MATURE_miRNA
+    vf = VariationFeature.new(:seq_region_id => 27518, :seq_region_start => 135895002, :seq_region_end => 135895002, :seq_region_strand => 1, :allele_string => "A/G", :variation_name => "rs11266800")
+    tv = vf.transcript_variations
+    assert_equal("WITHIN_MATURE_miRNA",tv[2].consequence_type)
+
+  # WITHIN_NON_CODING_GENE
+    vf = VariationFeature.new(:seq_region_id => 27506, :seq_region_start => 97601052, :seq_region_end => 97601052, :seq_region_strand => 1, :allele_string => "G/A", :variation_name => "rs13245475")
+    tv = vf.transcript_variations
+    assert_equal("WITHIN_NON_CODING_GENE",tv[1].consequence_type)
+
+  # COMPLEX_INDEL  
+    vf = VariationFeature.new(:seq_region_id => 27752, :seq_region_start => 37529, :seq_region_end => 37535, :seq_region_strand => 1, :allele_string => "CCACCCA/ACACCCG", :variation_name => "rs71228679")
+    tv = vf.transcript_variations
+    assert_equal("COMPLEX_INDEL",tv[0].consequence_type)  
+  
+  # ESSENTIAL_SPLICE_SITE
+    vf = VariationFeature.new(:seq_region_id => 27511, :seq_region_start => 818059, :seq_region_end => 818059, :seq_region_strand => 1, :allele_string => "G/T", :variation_name => "rs3888067")
+    tv = vf.transcript_variations
+    assert_equal("ESSENTIAL_SPLICE_SITE",tv[0].consequence_type)  
+
+  # SPLICE_SITE
+    vf = VariationFeature.new(:seq_region_id => 27506, :seq_region_start => 102301587, :seq_region_end => 102301587, :seq_region_strand => 1, :allele_string => "A/G", :variation_name => "rs434833")
+    tv = vf.transcript_variations
+    assert_equal("SPLICE_SITE",tv[5].consequence_type)  
+
+  # INTRONIC
+    vf = VariationFeature.new(:seq_region_id => 27506, :seq_region_start => 101165365, :seq_region_end => 101165365, :seq_region_strand => 1, :allele_string => "T/C", :variation_name => "rs1859633")
+    tv = vf.transcript_variations
+    assert_equal("INTRONIC",tv[2].consequence_type)  
+  
+  # FRAMESHIFT
+    vf = VariationFeature.new(:seq_region_id => 27511, :seq_region_start => 78958619, :seq_region_end => 78958618, :seq_region_strand => 1, :allele_string => "-/G", :variation_name => "rs35065683")
+    tv = vf.transcript_variations
+    assert_equal("FRAMESHIFT_CODING",tv[0].consequence_type)
+
+  # STOP_GAINED
+    vf = VariationFeature.new(:seq_region_id => 27516, :seq_region_start => 38262908, :seq_region_end => 38262908, :seq_region_strand => 1, :allele_string => "G/A", :variation_name => "rs72556299")
+    tv = vf.transcript_variations
+    assert_equal("STOP_GAINED",tv[-1].consequence_type)
+    
+  # STOP_LOST
+    vf = VariationFeature.new(:seq_region_id => 27511, :seq_region_start => 152770613, :seq_region_end => 152770613, :seq_region_strand => 1, :allele_string => "T/G", :variation_name => "rs41268500")
+    tv = vf.transcript_variations
+    assert_equal("STOP_LOST",tv[0].consequence_type)
+    
+  # SYNONYMOUS_CODING
+    vf = VariationFeature.new(:seq_region_id => 27506, :seq_region_start => 99688238, :seq_region_end => 99688238, :seq_region_strand => 1, :allele_string => "C/T", :variation_name => "rs11550651")
+    tv = vf.transcript_variations
+    assert_equal("SYNONYMOUS_CODING",tv[0].consequence_type)   
+
+  # NON_SYNONYMOUS_CODING
+    vf = VariationFeature.new(:seq_region_id => 27506, :seq_region_start => 99057720, :seq_region_end => 99057720, :seq_region_strand => 1, :allele_string => "G/A", :variation_name => "rs11545970")
+    tv = vf.transcript_variations
+    assert_equal("NON_SYNONYMOUS_CODING",tv[1].consequence_type)   
+     
+  end  
+  
+  # Checking CDNA coordinates calculation
+  
+  def test_genomic2cdna_fw # forward strand (variation rs67960011)
+    t = Ensembl::Core::Transcript.find_by_stable_id("ENST00000039007")
+    assert_equal(573,t.genomic2cdna(38260562))    
+  end
+  
+  def test_cdna2genomic_fw # forward strand (variation rs67960011)
+    t = Ensembl::Core::Transcript.find_by_stable_id("ENST00000039007")
+    assert_equal(38260562,t.cdna2genomic(573))
+  end
+  
+  def test_genomic2cdna_rev # reverse strand (variation rs11545970)
+    t = Ensembl::Core::Transcript.find_by_stable_id("ENST00000422429")
+    assert_equal(110,t.genomic2cdna(99057720))
+  end
+  
+  def test_cdna2genomic_rev # reverse strand (variation rs11545970)
+    t = Ensembl::Core::Transcript.find_by_stable_id("ENST00000422429")
+    assert_equal(99057720,t.cdna2genomic(110))
+  end
+
+
+end