ruby-ensembl-api 0.9.6 → 1.0

data/test/unit/{release_53 → release_60}/core/test_transform.rb

@@ -26,38 +26,38 @@ include Ensembl::Core
 class TransformOntoSameCoordinateSystem < Test::Unit::TestCase
 
   def setup
-    DBConnection.connect('homo_sapiens', 53)
+    DBConnection.connect('homo_sapiens', 60)
   end
   
   def teardown
     DBConnection.remove_connection
   end
 
-  def test_rev
-    source_gene = Gene.find(102634)
+  def test_fw
+    source_gene = Gene.find_by_stable_id("ENSG00000242450")
     target_gene = source_gene.transform('chromosome')
 
-    assert_equal('18', source_gene.seq_region.name)
-    assert_equal(17659657, source_gene.seq_region_start)
-    assert_equal(17659744, source_gene.seq_region_end)
-    assert_equal(-1, source_gene.seq_region_strand)
-    assert_equal('18', target_gene.seq_region.name)
-    assert_equal(17659657, target_gene.seq_region_start)
-    assert_equal(17659744, target_gene.seq_region_end)
-    assert_equal(-1, target_gene.seq_region_strand)
+    assert_equal('22', source_gene.seq_region.name)
+    assert_equal(24349643, source_gene.seq_region_start)
+    assert_equal(24349710, source_gene.seq_region_end)
+    assert_equal(1, source_gene.seq_region_strand)
+    assert_equal('22', target_gene.seq_region.name)
+    assert_equal(24349643, target_gene.seq_region_start)
+    assert_equal(24349710, target_gene.seq_region_end)
+    assert_equal(1, target_gene.seq_region_strand)
   end
 
-  def test_fw
-    source_gene = Gene.find(103817)
+  def test_rev
+    source_gene = Gene.find_by_stable_id("ENSG00000240339")
     target_gene = source_gene.transform('chromosome')
-    assert_equal('11', source_gene.seq_region.name)
-    assert_equal(66886461, source_gene.seq_region_start)
-    assert_equal(66886755, source_gene.seq_region_end)
-    assert_equal(1, source_gene.seq_region_strand)
-    assert_equal('11', target_gene.seq_region.name)
-    assert_equal(66886461, target_gene.seq_region_start)
-    assert_equal(66886755, target_gene.seq_region_end)
-    assert_equal(1, target_gene.seq_region_strand)
+    assert_equal('22', source_gene.seq_region.name)
+    assert_equal(24349560, source_gene.seq_region_start)
+    assert_equal(24349631, source_gene.seq_region_end)
+    assert_equal(-1, source_gene.seq_region_strand)
+    assert_equal('22', target_gene.seq_region.name)
+    assert_equal(24349560, target_gene.seq_region_start)
+    assert_equal(24349631, target_gene.seq_region_end)
+    assert_equal(-1, target_gene.seq_region_strand)
   end
 
 end

data/test/unit/release_60/variation/test_activerecord.rb

@@ -0,0 +1,213 @@
+#
+# = 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
+#
+# $Id:
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.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',60)
+  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(30351,n)
+    individual = Sample.find(12468).individual
+    assert_equal('Male',individual.gender)
+    i = Sample.find(13131).individual_genotype_multiple_bp
+    assert_equal(5,i.size)
+    assert_equal(1688213,i[0].variation_id)
+    syn = Sample.find(21).sample_synonym
+    assert_equal('6',syn.name)
+  end
+  
+  def test_individual
+    n = Individual.count(:all)
+    assert_equal(12307,n)
+  end
+  
+  def test_individual_genotype_multiple_bp
+    n = IndividualGenotypeMultipleBp.count(:all)
+    assert_equal(1009778,n)
+  end
+  
+  def test_compressed_genotype_single_bp
+    n = CompressedGenotypeSingleBp.count(:all)
+    assert_equal(67856517,n)
+  end
+  
+  def test_read_coverage
+    n = ReadCoverage.count(:all)
+    assert_equal(4183832,n)
+  end
+  
+  def test_population
+    n = Population.count(:all)
+    assert_equal(11673,n)
+    p = Population.find(236)
+    ind = p.individuals
+    assert_equal(653,ind.size)
+  end
+  
+  def test_variation
+    n = Variation.count(:all)
+    assert_equal(24623913,n)
+    
+    syn = Variation.find(712422).variation_synonyms
+    assert_equal(1,syn.size)
+    assert_equal('rs56673311',syn[0].name)
+    
+    flanking = Variation.find(10000).flanking_sequence
+    assert_equal(132077099,flanking.up_seq_region_start)
+    assert_equal(132077128,flanking.up_seq_region_end)
+    assert_equal(132077130,flanking.down_seq_region_start)
+    assert_equal(132077159,flanking.down_seq_region_end)
+    assert_equal(27517,flanking.seq_region_id)
+    assert_equal(1,flanking.seq_region_strand)
+    
+    ag = Variation.find(10000).allele_groups
+    assert_nil ag[0]
+    
+    pg = Variation.find(1234).population_genotypes
+    assert_equal(28,pg.size)
+    assert_equal('A',pg[0].allele_1)
+    assert_equal('A',pg[0].allele_2)
+    assert_equal(1,pg[0].frequency)
+    
+    a = Variation.find(115).alleles
+    assert_equal(14,a.size)
+    assert_equal('C',a[0].allele)
+    assert_equal(0.733,a[0].frequency)
+    
+    vf = Variation.find(5345540).variation_features[0]
+    assert_equal('C/T',vf.allele_string)
+    assert_equal('rs8192830',vf.variation_name)
+    assert_equal(27506,vf.seq_region_id)
+    assert_equal(139618573,vf.seq_region_start)
+    assert_equal(139618573,vf.seq_region_end)
+    assert_equal(1,vf.seq_region_strand)
+    
+    vg = Variation.find(1352735).variation_groups
+    assert_nil vg[0]
+    
+    i = Variation.find(243).individual_genotype_multiple_bps
+    assert_equal(68,i.size)
+  end
+  
+  def test_variation_feature
+    vf_sample = VariationFeature.find_by_variation_name('rs167125').samples
+    assert_equal(1,vf_sample.size)
+    assert_equal('CSHL-HAPMAP:HapMap-JPT',vf_sample[0].name)
+  end
+  
+  def test_variation_transcript
+    t = Variation.find_by_name('rs7671997').variation_features[0].transcript_variations
+    assert_equal(7,t.size)
+    assert_equal('WITHIN_NON_CODING_GENE',t[0].consequence_type)
+    assert_equal('5PRIME_UTR',t[2].consequence_type)
+    assert_equal(4079207,t[0].variation_feature_id)
+    transcript = t[0].transcript
+    assert_equal('processed_transcript',transcript.biotype)
+    assert_equal(2158121,transcript.seq_region_start)
+    assert_equal(2243848,transcript.seq_region_end)
+    assert_equal('ENST00000515357',transcript.stable_id)
+    e = transcript.exons
+    assert_equal('AGTGCGAGGCGCGCGGGGCACGGAGGGCGGTGGCGGCGGGCTCCTGCGAGAAGCAAGCGGAACTTCCTGAG',e[0].seq.upcase)
+
+  end
+  
+  def test_source
+    syn = Source.find(1).sample_synonyms
+    assert_equal(23061,syn.size)
+    
+    ag = Source.find(1).allele_groups
+    assert_nil ag[0]
+  end
+  
+  def test_variation_annotation
+    va = VariationAnnotation.find(95)
+    assert_equal(1756227,va.variation_id)
+    assert_equal('EGAS00000000060',va.local_stable_id)
+    assert_equal('rs2306027',va.variation_names)
+    assert_equal(0.218132812399633,va.risk_allele_freq_in_controls.to_f)    
+  end
+  
+  def test_phenotype
+    pheno = Phenotype.find(1527)
+    va = pheno.variation_annotations
+    assert_equal(14,va.size)
+    assert_equal('GATA6,CTAGE1,RBBP8,CABLES1',va[5].associated_gene)
+  end
+  
+  def test_structural_variation
+    sv = StructuralVariation.find(171276)
+    assert_equal('nsv429550',sv.variation_name)
+    assert_equal(224676,sv.seq_region_start)
+    assert_equal(44780026,sv.seq_region_end)
+    assert_equal('11',sv.seq_region.name)
+  end
+  
+  def test_population_genotype
+    v = Variation.find(1082)
+    pg = v.population_genotypes
+    assert_equal(41,pg.size)
+    assert_equal(0.6,pg[0].frequency)
+    pop = Population.find(132)
+    pg = pop.population_genotypes
+    assert_equal(1070,pg.size)
+  end
+  
+  def test_subsnp_handle
+    s = SubsnpHandle.find(946)
+    assert_equal('WIAF',s.handle)
+    pg = s.population_genotypes
+    assert_equal(2,pg.size)
+    assert_equal(0.4,pg[0].frequency)
+    alleles = s.alleles
+    assert_equal(2,alleles.size)
+    assert_equal('A',alleles[0].allele)
+    s = SubsnpHandle.find(107935890)
+    vs = s.variation_synonyms
+    assert_equal(1,vs.size)
+    assert_equal('ENSSNP10154320',vs[0].name)
+  end
+  
+  def test_variation_synonym
+    v = Variation.find(12659557)
+    vs = v.variation_synonyms
+    assert_equal(1,vs.size)
+    assert_equal('rs66792216',vs[0].name)
+  end
+  
+  def test_failed_description
+    v = Variation.find(15005920)
+    fd = v.failed_descriptions
+    assert_equal(1,fd.size)
+    assert_equal('Variation maps to more than 3 different locations',fd[0].description)
+  end
+  
+  
+end

data/test/unit/release_60/variation/test_consequence.rb

@@ -0,0 +1,158 @@
+#
+# = 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 '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
+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/unit/{release_56 → release_60}/variation/test_variation.rb

@@ -1,5 +1,5 @@
 #
-# = test/unit/release_50/variation/test_variation.tb - Unit test for Ensembl::Variation
+# = test/unit/release_56/variation/test_variation.tb - Unit test for Ensembl::Variation
 #
 # Copyright::   Copyright (C) 2009
 #               Francesco Strozzi <francesco.strozzi@gmail.com>
@@ -17,7 +17,7 @@ include Ensembl::Variation
 class TestVariation < Test::Unit::TestCase
   
   def setup
-    DBConnection.connect('homo_sapiens',56)
+    DBConnection.connect('homo_sapiens',60)
   end
   
   def teardown
@@ -39,13 +39,13 @@ class TestVariation < Test::Unit::TestCase
   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(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
@@ -53,16 +53,17 @@ class TestVariation < Test::Unit::TestCase
   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)
-
+    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
+end