ruby-ensembl-api 0.9.6 → 1.0

data/test/unit/release_53/core/test_slice.rb

@@ -1,47 +0,0 @@
-#
-# = 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
-#
-# $Id:
-
-require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
-
-require 'test/unit'
-require 'lib/ensembl'
-
-include Ensembl::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/unit/release_53/variation/test_activerecord.rb

@@ -1,145 +0,0 @@
-#
-# = 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
-#
-# $Id:
-require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.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',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]
-    
-    s = Source.count(9)
-    assert_equal(4,s.size)
-  end
-end

data/test/unit/release_53/variation/test_variation.rb

@@ -1,71 +0,0 @@
-#
-# = 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 '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 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

data/test/unit/release_56/core/test_project.rb

@@ -1,96 +0,0 @@
-#
-# = 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
-#
-# $Id:
-
-require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
-
-require 'test/unit'
-require 'lib/ensembl'
-
-include Ensembl::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/unit/release_56/core/test_transform.rb

@@ -1,63 +0,0 @@
-#
-# = 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
-#
-# $Id:
-
-require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
-
-require 'test/unit'
-
-require 'lib/ensembl'
-
-include Ensembl::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/unit/release_56/variation/test_activerecord.rb

@@ -1,142 +0,0 @@
-#
-# = 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
-#
-# $Id:
-require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.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',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)
-    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