bio-ensembl 1.1.0

data/test/release_53/core/test_project.rb

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+#
+# = 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', 53)
+    @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_53/core/test_project_human.rb

@@ -0,0 +1,61 @@
+#
+# = test/unit/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 AssemblyExceptions < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.connect('homo_sapiens', 53)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_chr_x
+    source_slice = Slice.fetch_by_region('chromosome','X', 2709497, 2709520)
+    assert_equal('tagttatagattaaaagaagttaa', source_slice.seq)
+  end
+
+  def test_slice_overlapping_PAR_and_allosome
+    source_slice = Slice.fetch_by_region('chromosome','Y',2709500,2709540)
+    target_slices = source_slice.project('contig')
+    assert_equal('contig::AC006209.25.1.141759:23323:23343:-1', target_slices[0].display_name)
+    assert_equal('contig::AC006040.3.1.186504:57272:57291:1', target_slices[1].display_name)
+  end
+
+  def test_seq_slice_overlapping_PAR
+    seq = ''
+    File.open("test/data/seq_y.fa").reject{|l| l=~/^>/}.each do |line|
+      line.chomp!
+      seq += line
+    end
+    seq.downcase!
+
+    source_slice = Slice.fetch_by_region('chromosome', 'Y', 2709497, 2709542)
+    assert_equal(seq.downcase, source_slice.seq)
+  end
+
+  # The MHC haplotypes for human are not implemented yet, so we raise an error
+  # in the code.
+  def test_seq_slice_overlapping_HAP
+    seq = ''
+    File.open('test/data/seq_c6qbl.fa').reject{|l| l=~/^>/}.each do |line|
+      line.chomp!
+      seq += line
+    end
+    seq.downcase!
+
+    source_slice = Slice.fetch_by_region('chromosome', 'c6_QBL', 33451191, 33451690)
+    assert_raise(NotImplementedError) {source_slice.seq}
+  end
+end

data/test/release_53/core/test_slice.rb

@@ -0,0 +1,42 @@
+#
+# = 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', 53)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_forward
+    seq1 = "AGAACCAACGAATTCGGAGATGAAGTCAGGTCTTCCAGTTCAGCCTGCGAGGAAGACAGGTGATCCGAATCCTAAGAATGCAAAAGATGGGCCGGGTGTGGTGGCTCATGCCTGTAATCCCAGCGCTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGGTCGGGAGGTTGAGACCAGACTGACCAACAACGGAGAAACCC"
+    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 = "GGGTTTCTCCGTTGTTGGTCAGTCTGGTCTCAACCTCCCGACCTCAGGTGATCTGCCTGCCTCGGCCTCCCAAAGCGCTGGGATTACAGGCATGAGCCACCACACCCGGCCCATCTTTTGCATTCTTAGGATTCGGATCACCTGTCTTCCTCGCAGGCTGAACTGGAAGACCTGACTTCATCTCCGAATTCGTTGGTTCT"
+    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
+
+end

data/test/release_53/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', 53)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+
+  def test_rev
+    source_gene = Gene.find(102634)
+    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)
+  end
+
+  def test_fw
+    source_gene = Gene.find(103817)
+    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)
+  end
+
+end

data/test/release_53/variation/test_activerecord.rb

@@ -0,0 +1,137 @@
+#
+# = 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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+include Ensembl::Variation
+
+class ActiveRecordVariation < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.connect('homo_sapiens',53)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_allele
+    allele = Allele.find(1)
+    assert_equal('C', allele.allele)
+    assert_equal(0.673913, allele.frequency)
+  end
+
+  def test_sample
+    n = Sample.count(:all)
+    assert_equal(15406,n)
+    individual = Sample.find(9146).individual
+    assert_equal('Female',individual.gender)
+    i = Sample.find(10128).individual_genotype_multiple_bp
+    assert_equal(990,i.size)
+    assert_equal(1533205,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(8658,n)
+  end
+  
+  def test_individual_genotype_multiple_bp
+    n = IndividualGenotypeMultipleBp.count(:all)
+    assert_equal(208579,n)
+  end
+  
+  def test_compressed_genotype_single_bp
+    n = CompressedGenotypeSingleBp.count(:all)
+    assert_equal(12580098,n)
+  end
+  
+  def test_read_coverage
+    n = ReadCoverage.count(:all)
+    assert_equal(9300776,n)
+  end
+  
+  def test_population
+    n = Population.count(:all)
+    assert_equal(6748,n)
+  end
+  
+  def test_variation
+    n = Variation.count(:all)
+    assert_equal(15872232,n)
+    
+    syn = Variation.find(84).variation_synonyms
+    assert_equal(6,syn.size)
+    assert_equal('TSC1239757',syn[0].name)
+    
+    flanking = Variation.find(10000).flanking_sequence
+    assert_equal(3652320,flanking.up_seq_region_start)
+    assert_equal(3652519,flanking.up_seq_region_end)
+    assert_equal(3652521,flanking.down_seq_region_start)
+    assert_equal(3652720,flanking.down_seq_region_end)
+    assert_equal(226033,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(0.593,a[0].frequency)
+    
+    vf = Variation.find(5345540).variation_features[0]
+    assert_equal('G/A',vf.allele_string)
+    assert_equal('rs8189278',vf.variation_name)
+    assert_equal(226044,vf.seq_region_id)
+    assert_equal(50727657,vf.seq_region_start)
+    assert_equal(50727657,vf.seq_region_end)
+    assert_equal(1,vf.seq_region_strand)
+    
+    vg = Variation.find(1352735).variation_groups
+    assert_nil vg[0]
+    
+    i = Variation.find(1533205).individual_genotype_multiple_bps
+    assert_equal(41,i.size)
+  end
+  
+  def test_variation_feature
+    vf_sample = VariationFeature.find(8).samples
+    assert_equal(6,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(2,t.size)
+    transcript = t[0].transcript
+    assert_equal('protein_coding',transcript.biotype) 
+    assert_equal(2199894,transcript.seq_region_start)
+    assert_equal(2213658,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(15385,syn.size)
+    
+    ag = Source.find(1).allele_groups
+    assert_nil ag[0]
+  end
+end

data/test/release_53/variation/test_variation.rb

@@ -0,0 +1,66 @@
+#
+# = 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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+include Ensembl::Variation
+
+class TestVariation < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.connect('homo_sapiens',53)
+  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(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',1,50000,50300)
+    variations = slice.get_variation_features
+    assert_equal(8,variations.size)
+    
+    assert_equal('rs987669',variations[0].variation_name)
+    assert_equal('ENSSNP4691381',variations[1].variation_name)
+    assert_equal('rs2854665',variations[2].variation_name)
+    assert_equal('rs62637816',variations[3].variation_name)
+    assert_equal('ENSSNP9996411',variations[4].variation_name)
+    assert_equal('rs62637817',variations[5].variation_name)
+    assert_equal('rs2691281',variations[6].variation_name)
+    assert_equal('ENSSNP4068519',variations[7].variation_name)
+
+  end
+  
+  
+  
+end