bio-ensembl 1.1.0

data/test/release_60/variation/test_consequence.rb

@@ -0,0 +1,153 @@
+#
+# = 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
+DBConnection.connect('homo_sapiens',60)
+
+class TestVariation < Test::Unit::TestCase
+    
+  def test_intergenic  
+  # 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)
+  end  
+
+  def test_3prime
+  # 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[0].consequence_type) 
+  end
+  
+  def test_5prime
+  # 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) 
+  end
+  
+  def test_upstream
+  # 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)
+  end
+  
+  def test_downstream
+  # 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[-1].consequence_type)
+  end
+  
+  def test_mirna
+  # WITHIN_MATURE_miRNA
+    vf = VariationFeature.new(:seq_region_id => 27527, :seq_region_start => 175878848, :seq_region_end => 175878848, :seq_region_strand => 1, :allele_string => "C/T", :variation_name => "rs12716316")
+    tv = vf.transcript_variations
+    assert_equal("WITHIN_MATURE_miRNA",tv[-1].consequence_type)
+  end
+
+
+  def test_non_coding
+  # 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)
+  end  
+
+  def test_complex_indel
+  # COMPLEX_INDEL
+    vf = VariationFeature.new(:seq_region_id => 27515, :seq_region_start => 31902068, :seq_region_end => 31902095, :seq_region_strand => 1, :allele_string => "GTGGACAGGGTCAGGAATCAGGAGTCTG/-", :variation_name => "rs9332736")
+    tv = vf.transcript_variations
+    assert_equal("COMPLEX_INDEL",tv[6].consequence_type)  
+  end
+  
+  def test_essential_splice
+  # ESSENTIAL_SPLICE_SITE
+    vf = VariationFeature.new(:seq_region_id => 27515, :seq_region_start => 33385862, :seq_region_end => 33385862, :seq_region_strand => 1, :allele_string => "A/G", :variation_name => "GA005718")
+    tv = vf.transcript_variations
+    assert_equal("ESSENTIAL_SPLICE_SITE",tv[21].consequence_type)  
+  end  
+    
+  def test_splice_site
+  # 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)  
+  end
+
+  def test_intronic
+  # INTRONIC
+    vf = VariationFeature.new(:seq_region_id => 27515, :seq_region_start => 31902068, :seq_region_end => 31902095, :seq_region_strand => 1, :allele_string => "GTGGACAGGGTCAGGAATCAGGAGTCTG/-", :variation_name => "rs9332736")
+    tv = vf.transcript_variations
+    assert_equal("INTRONIC",tv[3].consequence_type)  
+  end
+  
+  def test_frameshift
+  # 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[1].consequence_type)
+  end
+  
+  def test_stop_gained
+  # 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)
+  end
+  
+  def test_stop_lost  
+  # 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)
+  end
+  
+  def test_synonymous  
+  # 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[5].consequence_type)   
+  end
+  
+  def test_non_synonymous
+  # 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[9].consequence_type)
+    assert_equal("A/V",tv[9].peptide_allele_string)
+  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

data/test/release_60/variation/test_variation.rb

@@ -0,0 +1,64 @@
+#
+# = 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',60)
+  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(29712970,up.start)
+    assert_equal(29713369,up.stop)
+    assert_equal(29713371,down.start)
+    assert_equal(29713770,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',1,100834,101331)
+    variations = slice.get_variation_features
+    assert_equal(1,variations.size)
+    assert_equal('rs78180088',variations[0].variation_name)
+  end
+  
+  def test_slice_structural_variation
+    slice = Ensembl::Core::Slice.fetch_by_region('chromosome',11,60125,320837)
+    sv = slice.get_structural_variations
+    assert_equal(16,sv.size)
+    assert_equal('nsv8753',sv[0].variation_name)
+  end
+  
+  
+  
+end

data/test/release_62/core/test_gene.rb

@@ -0,0 +1,42 @@
+#
+# = test/unit/release_62/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', 62)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_stable_id
+    ids = %w(ENSG00000243485 ENSG00000221311 ENSG00000237613 ENSG00000240361 ENSG00000186092)
+    genes = Gene.find_by_stable_id(ids)
+    assert_equal(5,genes.size)
+    assert_equal("ENSG00000186092",genes[0].stable_id)
+    assert_equal(65882,genes[0].seq_region_start)
+    assert_equal(70008,genes[0].seq_region_end)
+    assert_equal("Olfactory receptor 4F4 [Source:UniProtKB/Swiss-Prot;Acc:Q96R69]",genes[0].description)
+    
+    gene = Gene.find_by_stable_id("ENSG00000186092")
+    genes = Gene.find_by_stable_id(ids)
+    assert_equal("ENSG00000186092",gene.stable_id)
+    assert_equal(65882,gene.seq_region_start)
+    assert_equal(70008,gene.seq_region_end)
+    assert_equal("Olfactory receptor 4F4 [Source:UniProtKB/Swiss-Prot;Acc:Q96R69]",gene.description)
+  end
+  
+  
+end

data/test/release_62/variation/test_activerecord.rb

@@ -0,0 +1,86 @@
+#
+# = 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',62)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_study
+    s = Study.find(134)
+    assert_equal(13,s.source_id)
+    assert_equal("Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.",s.description)
+    assert_equal("pubmed/17554300",s.external_reference)
+    assert_equal("GWAS",s.study_type)
+    a = s.associate_studies
+    assert_equal(17,a.size)
+
+    study = Study.find_by_name "estd19"
+    assert_equal("Ahn 2009 \"The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.\" PMID:19470904 [remapped from build NCBI36]",study.description)
+    assert_equal("ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd19_Ahn_et_al_2009",study.url)
+    assert_equal("pubmed/19470904",study.external_reference)
+    struct = study.structural_variations
+    assert_equal(4281,struct.size)
+    assert_equal("esv9167",struct[0].variation_name)
+    assert_equal("SV",struct[0].sv_class)
+    assert_equal(27515,struct[0].seq_region_id)
+    assert_equal(3478018,struct[0].seq_region_start)
+    assert_equal(3478196,struct[0].seq_region_end)
+    
+    study = Study.find(33)
+    ann = study.variation_annotations
+    assert_equal(17,ann.size)
+    assert_equal(30235485,ann[0].variation_id)
+    assert_equal("Intergenic",ann[0].associated_gene)
+    assert_equal("rs11206801-A",ann[0].associated_variant_risk_allele)
+    assert_equal("6E-8",ann[0].p_value)
+    
+  end
+  
+  def test_protein_info
+    i = ProteinInfo.find_by_transcript_stable_id "ENST00000358183"
+    position = i.protein_positions
+    assert_equal(1195,position.size)
+    assert_equal(1,position[0].position)
+    assert_equal("M",position[0].amino_acid)
+    assert_equal(4.32,position[0].sift_median_conservation)
+    assert_equal(12,position[0].sift_num_sequences_represented)
+  end
+  
+  def test_predictions
+    i = ProteinInfo.find_by_transcript_stable_id "ENST00000228777"
+    position = i.protein_positions[3]
+    sift = position.sift_predictions[0]
+    assert_equal("A",sift.amino_acid)
+    assert_equal("tolerated",sift.prediction)
+    assert_equal(0.05,sift.score)
+    
+    polyphen = position.polyphen_predictions[0]
+    assert_equal("A",polyphen.amino_acid)
+    assert_equal("benign",polyphen.prediction)
+    assert_equal(0.006,polyphen.probability)
+  end
+  
+  def test_structural_variation
+    s = StructuralVariation.find_by_variation_name "esv9167"
+    supp = s.supporting_structural_variations
+    assert_equal(1,supp.size)
+    assert_equal("essv31608",supp[0].name)
+  end
+  
+end

data/test/release_62/variation/test_consequence.rb

@@ -0,0 +1,191 @@
+#
+# = test/unit/release_62/variation/test_consequence.tb - Unit test for Ensembl::Variation
+#
+# Copyright::   Copyright (C) 2011
+#               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',62)
+
+class TestVariation < Test::Unit::TestCase
+
+  def test_3prime
+    vf = VariationFeature.new(:seq_region_id => 27519, :seq_region_start => 299504, :seq_region_end => 299504, :seq_region_strand => 1, :allele_string => "T/C", :variation_name => "rs78048681")
+    tv = vf.transcript_variations
+    assert_equal("3_prime_UTR_variant", tv[0].consequence_types) 
+  end
+
+  def test_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_variant",tv[0].consequence_types)
+  end
+
+  def test_splice_acceptor
+    vf = VariationFeature.new(:seq_region_id => 27511, :seq_region_start => 1248331, :seq_region_end => 1248331, :seq_region_strand => 1, :allele_string => "T/A", :variation_name => "rs113769441")
+    tv = vf.transcript_variations
+    assert_equal("splice_acceptor_variant", tv[34].consequence_types)
+    assert_equal("ENST00000527098",tv[43].feature_stable_id)
+  end
+
+  def test_splice_donor
+    vf = VariationFeature.new(:seq_region_id => 27511, :seq_region_start => 1247605, :seq_region_end => 1247605, :seq_region_strand => 1, :allele_string => "C/G", :variation_name => "rs113643330")
+    tv = vf.transcript_variations
+    assert_equal("splice_donor_variant", tv[34].consequence_types)
+    assert_equal("ENST00000545578",tv[34].feature_stable_id)
+  end
+
+  def test_complex_change_in_transcript
+    vf = VariationFeature.new(:seq_region_id => 27509, :seq_region_start => 4837133, :seq_region_end => 4837210, :seq_region_strand => 1, :allele_string => "-/GAGCCCACCTCAGAGCCCGCCCCCAGCCCGACCACCCCG", :variation_name => "rs41439349")
+    tv = vf.transcript_variations
+    assert_equal("complex_change_in_transcript", tv[0].consequence_types)
+    assert_equal("ENST00000438881",tv[0].feature_stable_id)
+  end
+
+  def test_stop_lost
+    vf = VariationFeature.new(:seq_region_id => 27509, :seq_region_start => 4701716, :seq_region_end => 4701716, :seq_region_strand => 1, :allele_string => "G/T", :variation_name => "rs1804248")
+    tv = vf.transcript_variations
+    assert_equal("stop_lost", tv[0].consequence_types)
+    assert_equal("ENST00000270586",tv[0].feature_stable_id)
+  end
+
+  def test_coding_sequence
+    vf = VariationFeature.new(:seq_region_id => 27509, :seq_region_start => 4836003, :seq_region_end => 4836003, :seq_region_strand => 1, :allele_string => "A/HGMD_MUTATION", :variation_name => "rs1804248")
+    tv = vf.transcript_variations
+    assert_equal("coding_sequence_variant", tv[0].consequence_types)
+    assert_equal("ENST00000438881",tv[0].feature_stable_id)
+  end
+
+  def test_non_synonymous_codon
+    vf = VariationFeature.new(:seq_region_id => 27519, :seq_region_start => 313785, :seq_region_end => 313785, :seq_region_strand => 1, :allele_string => "T/C", :variation_name => "rs112982618")
+    tv = vf.transcript_variations
+    assert_equal("non_synonymous_codon", tv[12].consequence_types)
+    assert_equal("ENST00000535347",tv[12].feature_stable_id)
+    assert_equal("N/S",tv[12].pep_allele_string)
+  end
+
+  def test_stop_gained
+    vf = VariationFeature.new(:seq_region_id => 27509, :seq_region_start => 4836976, :seq_region_end => 4836976, :seq_region_strand => 1, :allele_string => "G/A", :variation_name => "rs121908061")
+    tv = vf.transcript_variations
+    assert_equal("stop_gained", tv[1].consequence_types)
+    assert_equal("ENST00000329125",tv[1].feature_stable_id)
+  end
+
+  def test_synonymous_codon
+    vf = VariationFeature.new(:seq_region_id => 27519, :seq_region_start => 313751, :seq_region_end => 313751, :seq_region_strand => 1, :allele_string => "T/C", :variation_name => "rs11609900")
+    tv = vf.transcript_variations
+    assert_equal("synonymous_codon", tv[12].consequence_types)
+    assert_equal("ENST00000535347",tv[12].feature_stable_id)
+  end
+
+  def test_frameshift_variant
+    vf = VariationFeature.new(:seq_region_id => 27527, :seq_region_start => 156589990, :seq_region_end => 156589989, :seq_region_strand => 1, :allele_string => "-/C", :variation_name => "rs35703155")
+    tv = vf.transcript_variations
+    assert_equal("frameshift_variant", tv[-1].consequence_types)
+    assert_equal("ENST00000302938",tv[-1].feature_stable_id)
+  end
+
+  def test_nc_transcript
+    vf = VariationFeature.new(:seq_region_id => 27523, :seq_region_start => 43139829, :seq_region_end => 43139829, :seq_region_strand => 1, :allele_string => "G/T", :variation_name => "rs4736847")
+    tv = vf.transcript_variations
+    assert_equal("nc_transcript_variant", tv[0].consequence_types)
+    assert_equal("ENST00000522985",tv[0].feature_stable_id)
+  end
+
+  def test_mature_miRNA
+    vf = VariationFeature.new(:seq_region_id => 27504, :seq_region_start => 18204679, :seq_region_end => 18204679, :seq_region_strand => 1, :allele_string => "T/C", :variation_name => "rs10832898")
+    tv = vf.transcript_variations
+    assert_equal("mature_miRNA_variant", tv[1].consequence_types)
+    assert_equal("ENST00000408110",tv[1].feature_stable_id)
+  end
+
+  def test_5prime
+    vf = VariationFeature.new(:seq_region_id => 27509, :seq_region_start => 4835627, :seq_region_end => 4835627, :seq_region_strand => 1, :allele_string => "C/T", :variation_name => "rs56337033")
+    tv = vf.transcript_variations
+    assert_equal("5_prime_UTR_variant", tv[1].consequence_types)
+    assert_equal("ENST00000329125",tv[1].feature_stable_id)
+  end
+
+  def test_incomplete_terminal_codon
+    vf = VariationFeature.new(:seq_region_id => 27525, :seq_region_start => 118397884, :seq_region_end => 118397884, :seq_region_strand => 1, :allele_string => "A/G", :variation_name => "rs4751995")
+    tv = vf.transcript_variations
+    assert_equal("incomplete_terminal_codon_variant", tv[4].consequence_types)
+    assert_equal("ENST00000433618",tv[4].feature_stable_id)
+  end
+
+  #def test_splice_region # THE EXAMPLES WITHIN HUMAN DATABASE CAN'T BE USED AS TEST
+  #  vf = VariationFeature.new(:seq_region_id => 27505, :seq_region_start => 14743754, :seq_region_end => 14743754, :seq_region_strand => 1, :allele_string => "C/T", :variation_name => "rs74734987")
+  #  tv = vf.transcript_variations
+  #  tv.each {|var| puts var.consequence_types+" "+var.feature_stable_id}
+  #  assert_equal("splice_region_variant", tv[0].consequence_types)
+  #  assert_equal("ENST00000540061",tv[0].feature_stable_id)
+  #end
+
+  def test_intron_variant
+    vf = VariationFeature.new(:seq_region_id => 27519, :seq_region_start => 312127, :seq_region_end => 312127, :seq_region_strand => 1, :allele_string => "G/T", :variation_name => "rs75380489")
+    tv = vf.transcript_variations
+    assert_equal("intron_variant", tv[0].consequence_types)
+    assert_equal("ENST00000228777",tv[0].feature_stable_id)
+  end
+
+  def test_5KB_downstream_variant
+    vf = VariationFeature.new(:seq_region_id => 27519, :seq_region_start => 300500, :seq_region_end => 300500, :seq_region_strand => 1, :allele_string => "T/C", :variation_name => "rs10128942")
+    tv = vf.transcript_variations
+    assert_equal("5KB_downstream_variant", tv[15].consequence_types)
+    assert_equal("ENST00000535498",tv[15].feature_stable_id)
+  end
+
+  def test_2KB_upstream_variant
+    vf = VariationFeature.new(:seq_region_id => 27519, :seq_region_start => 300500, :seq_region_end => 300500, :seq_region_strand => 1, :allele_string => "T/C", :variation_name => "rs10128942")
+    tv = vf.transcript_variations
+    assert_equal("2KB_upstream_variant", tv[-1].consequence_types)
+    assert_equal("ENST00000544067",tv[-1].feature_stable_id) 
+  end
+
+  def test_5KB_upstream_variant
+    vf = VariationFeature.new(:seq_region_id => 27511, :seq_region_start => 242503860, :seq_region_end => 242503860, :seq_region_strand => 1, :allele_string => "G/T", :variation_name => "rs12727465")
+    tv = vf.transcript_variations
+    assert_equal("5KB_upstream_variant", tv[-1].consequence_types)
+    assert_equal("ENST00000447710",tv[-1].feature_stable_id)
+  end
+  
+  def test_500B_downstream_variant
+    vf = VariationFeature.new(:seq_region_id => 27523, :seq_region_start => 43139379, :seq_region_end => 43139379, :seq_region_strand => 1, :allele_string => "T/A", :variation_name => "rs114568988")
+    tv = vf.transcript_variations
+    assert_equal("500B_downstream_variant", tv[0].consequence_types)
+    assert_equal("ENST00000522985",tv[0].feature_stable_id)
+  end
+  
+  def test_initiator_codon_change
+    vf = VariationFeature.new(:seq_region_id => 27509, :seq_region_start => 3450007, :seq_region_end => 3450007, :seq_region_strand => 1, :allele_string => "C/T", :variation_name => "rs390804")
+    tv = vf.transcript_variations
+    assert_equal("initiator_codon_change", tv[1].consequence_types)
+    assert_equal("ENST00000430263",tv[1].feature_stable_id)
+  end
+
+  def test_stop_retained
+    vf = VariationFeature.new(:seq_region_id => 27515, :seq_region_start => 138202334, :seq_region_end => 138202334, :seq_region_strand => 1, :allele_string => "G/A", :variation_name => "COSM35908")
+    tv = vf.transcript_variations
+    assert_equal("stop_retained_variant", tv[0].consequence_types)
+    assert_equal("ENST00000535574",tv[0].feature_stable_id)
+  end
+
+  def test_inframe_codon_gain
+    vf = VariationFeature.new(:seq_region_id => 27509, :seq_region_start => 636321, :seq_region_end => 636320, :seq_region_strand => 1, :allele_string => "-/CTC", :variation_name => "rs111405529")
+    tv = vf.transcript_variations
+    assert_equal("inframe_codon_gain", tv[1].consequence_types)
+    assert_equal("ENST00000451373",tv[1].feature_stable_id)
+  end
+
+  def test_inframe_codon_loss
+    vf = VariationFeature.new(:seq_region_id => 27509, :seq_region_start => 4837133, :seq_region_end => 4837210, :seq_region_strand => 1, :allele_string => "GAGCCCACCTCAGAGCCCGCCCCCAGCCCGACCACCCCGGAGCCCACCTCAGAGCCCGCCCCCAGCCCGACCACCCCA/-", :variation_name => "rs41439349")
+    tv = vf.transcript_variations
+    assert_equal("inframe_codon_loss", tv[1].consequence_types)
+    assert_equal("ENST00000329125",tv[1].feature_stable_id)
+  end
+
+end