ruby-ensembl-api 0.9.6 → 1.0

data/test/unit/release_50/variation/test_activerecord.rb

@@ -1,143 +0,0 @@
-#
-# = test/unit/release_50/variation/test_activerecord.rb - Unit test for Ensembl::Variation
-#
-# Copyright::   Copyright (C) 2008 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
-DBConnection.connect('homo_sapiens',50)
-
-class ActiveRecordVariation < Test::Unit::TestCase
-  
-  def test_allele
-    allele = Allele.find(1)
-    assert_equal('T', allele.allele)
-    assert_equal(0.04, allele.frequency)
-  end
-  
-  def test_allele_group
-    n = AlleleGroup.count(:all)
-    assert_equal(0, n)
-  end
-
-  def test_sample
-    n = Sample.count(:all)
-    assert_equal(12385,n)
-    individual = Sample.find(5499).individual
-    assert_equal('Male',individual.gender)
-    i = Sample.find(6201).individual_genotype_multiple_bp
-    assert_equal(1256,i.size)
-    assert_equal(548383,i[0].variation_id)
-    syn = Sample.find(17).sample_synonym
-    assert_equal('5',syn.name)
-  end
-  
-  def test_individual
-    n = Individual.count(:all)
-    assert_equal(7769,n)
-  end
-  
-  def test_individual_genotype_multiple_bp
-    n = IndividualGenotypeMultipleBp.count(:all)
-    assert_equal(835033,n)
-  end
-  
-  def test_compressed_genotype_single_bp
-    n = CompressedGenotypeSingleBp.count(:all)
-    assert_equal(12473477,n)
-  end
-  
-  def test_read_coverage
-    n = ReadCoverage.count(:all)
-    assert_equal(9328349,n)
-  end
-  
-  def test_population
-    n = Population.count(:all)
-    assert_equal(4616,n)
-  end
-  
-  def test_variation
-    n = Variation.count(:all)
-    assert_equal(13383219,n)
-    
-    syn = Variation.find(27).variation_synonyms
-    assert_equal('SNP001745772',syn[0].name)
-    
-    flanking = Variation.find(130).flanking_sequence
-    assert_equal(24910767,flanking.up_seq_region_start)
-    assert_equal(24911281,flanking.up_seq_region_end)
-    assert_equal(24911283,flanking.down_seq_region_start)
-    assert_equal(24911367,flanking.down_seq_region_end)
-    assert_equal(226030,flanking.seq_region_id)
-    assert_equal(1,flanking.seq_region_strand)
-    
-    ag = Variation.find(130).allele_groups
-    assert_nil ag[0]
-    
-    pg = Variation.find(1125).population_genotypes
-    assert_equal(26,pg.size)
-    assert_equal('A',pg[0].allele_1)
-    assert_equal('A',pg[0].allele_2)
-    assert_equal(0.2,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('G/A',vf.allele_string)
-    assert_equal('rs8175337',vf.variation_name)
-    assert_equal(226028,vf.seq_region_id)
-    assert_equal(10052344,vf.seq_region_start)
-    assert_equal(10052344,vf.seq_region_end)
-    assert_equal(1,vf.seq_region_strand)
-    
-    vg = Variation.find(1352735).variation_groups
-    assert_nil vg[0]
-    
-    i = Variation.find(1352735).individual_genotype_multiple_bps
-    assert_equal(31,i.size)
-  end
-  
-  def test_variation_feature
-    vf_sample = VariationFeature.find(4571).samples
-    assert_equal(5,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(5,t.size)
-    assert_equal(69644,t[0].transcript_id)
-    transcript = t[0].transcript
-    assert_equal('protein_coding',transcript.biotype) 
-    assert_equal(2050017,transcript.seq_region_start)
-    assert_equal(2148813,transcript.seq_region_end)
-    assert_equal('ENST00000382857',transcript.stable_id)
-    e = transcript.exons
-    assert_equal('ATGGCTGTGGGGAGCCAG',e[0].seq.upcase)
-  end
-  
-  def test_source
-    syn = Source.find(1).sample_synonyms
-    assert_equal('2',syn[0].name)
-    
-    ag = Source.find(1).allele_groups
-    assert_nil ag[0]
-    
-    v = Source.find(6).variations
-    assert_equal(19,v.size)
-    assert_equal('SNP_A-8319323',v[0].name)
-  end
-end

data/test/unit/release_50/variation/test_variation.rb

@@ -1,84 +0,0 @@
-#
-# = test/unit/release_50/variation/test_variation.tb - Unit test for Ensembl::Variation
-#
-# Copyright::   Copyright (C) 2008 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',50)
-
-class TestVariation < Test::Unit::TestCase
-  
-  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',1,50000,51000)
-    variations = slice.get_variation_features
-    assert_equal(9,variations.size)
-    assert_equal('ENSSNP4691381',variations[0].variation_name)
-    assert_equal('ENSSNP9996411',variations[1].variation_name)
-    assert_equal('rs2691281',variations[2].variation_name)
-    assert_equal('ENSSNP4068519',variations[3].variation_name)
-    assert_equal('ENSSNP230814',variations[4].variation_name)
-    assert_equal('ENSSNP4010737',variations[5].variation_name)
-    assert_equal('rs2531295',variations[6].variation_name)
-    assert_equal('ENSSNP5092147',variations[7].variation_name)
-    assert_equal('ENSSNP5346602',variations[8].variation_name)
-    
-    genotyped = slice.get_genotyped_variation_features
-    assert_equal(7,genotyped.size)
-    assert_equal('ENSSNP4691381',genotyped[0].variation_name)
-    assert_equal('genotyped',genotyped[0].flags)
-    assert_equal('ENSSNP9996411',genotyped[1].variation_name)
-    assert_equal('genotyped',genotyped[1].flags)
-    assert_equal('ENSSNP4068519',genotyped[2].variation_name)
-    assert_equal('genotyped',genotyped[2].flags)
-    assert_equal('ENSSNP230814',genotyped[3].variation_name)
-    assert_equal('genotyped',genotyped[3].flags)
-    assert_equal('ENSSNP4010737',genotyped[4].variation_name)
-    assert_equal('genotyped',genotyped[4].flags)
-    assert_equal('ENSSNP5092147',genotyped[5].variation_name)
-    assert_equal('genotyped',genotyped[5].flags)
-    assert_equal('ENSSNP5346602',genotyped[6].variation_name)
-    assert_equal('genotyped',genotyped[6].flags)
-    
-    v = variations[0].variation
-    assert_equal(16366812,v.variation_id)
-  end
-  
-  
-  
-end

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

@@ -1,66 +0,0 @@
-#
-# = test/unit/release_53/core/test_gene.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 TestGene < Test::Unit::TestCase
-  
-  def setup
-    DBConnection.connect('homo_sapiens', 53)
-  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(39629687,g.start)
-    assert_equal(39714240,g.stop)
-    assert_equal(1,g.strand)
-    assert_equal(84554,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(1,t.size)
-    assert_equal("ENST00000005257",t[0].stable_id)
-    t = t[0]
-    assert_equal(2792,t.seq.length)
-  end
-  
-  def test_exons
-    t = Transcript.find_by_stable_id("ENST00000005257")
-    e = t.exons
-    assert_equal(5,e.size)
-    assert_equal("ENSE00001324495",e[0].stable_id)
-    seq1 = "AAGTGATCTGTGGCGGCTGCTGCAGAGCCGCCAGGAGGAGGGTGGATCTCCCCAGAGCAAAGCGTCGGAGTCCTCCTCCTCCTTCTCCTCCTCCTCCTCCTCCTCCTCCAGCCGCCCAGGCTCCCCCGCCACCCGTCAGACTCCTCCTTCGACCGCTCCCGGCGCGGGGCCTTCCAGGCGACAAGGACCGAGTACCCTCCGGCCGGAGCCACGCAGCCGCGGCTTCCGGAGCCCTCGGGGCGGCGGACTGGCTCGCGGTGCAG"
-    assert_equal(seq1,e[0].seq.upcase)
-    assert_equal(39629687,e[0].start)
-    assert_equal(39629949,e[0].stop)
-    assert_equal("ENSE00000832451",e[1].stable_id)
-    seq2 = "ATTCTTCTTAATCCTTTGGTGAAAACTGAGACACAAAATGGCTGCAAATAAGCCCAAGGGTCAGAATTCTTTGGCTTTACACAAAGTCATCATGGTGGGCAGTGGTGGCGTGGGCAAGTCAGCTCTGACTCTACAGTTCATGTACGATGAG"
-    assert_equal(seq2,e[1].seq.upcase)
-    assert_equal(39692755,e[1].start)
-    assert_equal(39692905,e[1].stop)
-  end
-
-end

data/test/unit/release_53/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', 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/unit/release_53/core/test_project_human.rb

@@ -1,65 +0,0 @@
-#
-# = 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
-#
-# $Id:
-require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
-require 'test/unit'
-require 'lib/ensembl'
-
-include Ensembl::Core
-
-class 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/unit/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/unit/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