ruby-ensembl-api 0.9.6

data/test/unit/ensembl_genomes/test_gene.rb

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+#
+# = test/unit/release_53/ensembl_genomes/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.ensemblgenomes_connect('pyrococcus_collection',3) 
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_find_gene
+    g = Gene.find_by_stable_id("EBPYRG00000005609")
+    assert_equal("EBPYRG00000005609",g.stable_id)
+    assert_equal(1195302,g.start)
+    assert_equal(1196675,g.stop)
+    assert_equal("Chromosome",g.seq_region.name)
+    assert_equal("ATGAATAGGAGCTTGTACTTGATTTTTATAATTGTAGGATATACTTTGGGAATATGGACA",g.seq.slice(0,60).upcase)
+  end
+  
+  def test_find_transcript
+    g = Gene.find_by_stable_id("EBPYRG00000005609")
+    t = g.transcripts
+    assert_equal("EBPYRT00000005610",t[0].stable_id)
+  end
+  
+  def test_find_exons
+    g = Gene.find_by_stable_id("EBPYRG00000005609")
+    t = g.transcripts
+    e = t[0].exons
+    assert_equal("EBPYRE00000005617",e[0].stable_id)
+    assert_equal("ATGAATAGGAGCTTGTACTTGATTTTTATAATTGTAGGATATACTTTGGGAATATGGACA",e[0].seq.slice(0,60).upcase)  	
+  end
+  
+end

data/test/unit/ensembl_genomes/test_slice.rb

@@ -0,0 +1,71 @@
+#
+# = test/unit/release_53/ensembl_genomes/test_collection.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 teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_fetch_by_region
+    DBConnection.ensemblgenomes_connect('mycobacterium_collection',3)
+    slice = Slice.fetch_by_region('chromosome',"Chromosome",183617,183716,1,"Mycobacterium tuberculosis H37Rv")
+    assert_equal("GCGCCATGACAGATCCGCAGACGCAGAGCACCAGGGTCGGGGTGGTTGCCGAGTCGGGGCCCGACGAACGACGGGTCGCGCTGGTTCCCAAGGCGGTCGC",slice.seq.upcase)
+    
+    slice = Slice.fetch_by_region('chromosome',"Chromosome",4285422,4285521,1,"Mycobacterium paratuberculosis")
+    assert_equal("GGTGTTAACGGCCGAAAGGTGGTTGAAAGATCGGCGGAATCGGGCGCACCCGGGTGGTCGTCGACGCCGCGCTGGTGGTGCTCGGCTGCGCCGTCGTGGT",slice.seq.upcase)
+    
+    slice = Slice.fetch_by_region('chromosome',"Chromosome",2667164,2667263,1,"Mycobacterium paratuberculosis")
+    assert_equal("GTTCCACCTGCCGATCGTCTTCCTCGCCGATAACCCGGGCATGCTGCCCGGCAGCCGGTCCGAACGCAGCGGTGTGCTGCGCGCCGGCGCGCGGATGTTC",slice.seq.upcase)
+  end
+  
+  def test_fetch_genes_from_slice
+    DBConnection.ensemblgenomes_connect('mycobacterium_collection',3)
+    slice = Slice.fetch_by_region('chromosome',"Chromosome",620900,622130 ,1,"Mycobacterium tuberculosis H37Rv")
+    genes = slice.genes
+    assert_equal("EBMYCG00000001929",genes[0].stable_id)
+    
+    slice = Slice.fetch_by_region('chromosome',"Chromosome",923890,925120 ,1,"Mycobacterium paratuberculosis")
+    genes = slice.genes
+    assert_equal("EBMYCG00000037956",genes[0].stable_id)
+  end
+  
+  def test_new_db_and_reverse_slice
+    DBConnection.ensemblgenomes_connect('escherichia_coli_K12',3)
+    slice = Slice.fetch_by_region('chromosome',"Chromosome",831691,831790,-1)
+    assert_equal("AAACGATGCTTACTGGGGAGACGGTGGTCATGGTAAGGGCAAGAATCGACTGGGCTACCTTTTAATGGAGTTGCGCGAACAATTGGCTATAGAGAAGTAA",slice.seq.upcase)
+    
+    slice = Slice.fetch_by_region('chromosome',"Chromosome",831690,832175,-1)
+    genes = slice.genes
+    assert_equal("EBESCG00000001341",genes[0].stable_id)
+  end
+  
+  def test_fetch_all
+    DBConnection.ensemblgenomes_connect('bacillus_anthracis_Sterne',3)
+    slices = Slice.fetch_all('chromosome')
+    assert_equal(5228663,slices[0].length)
+  end
+  
+  def test_error_species
+    DBConnection.ensemblgenomes_connect('bacillus_collection',3)
+    assert_raise ArgumentError do 
+      Slice.fetch_by_region('chromosome',"Chromosome",831690,832175,1,"Wrong specie name")
+    end
+  end
+
+end

data/test/unit/ensembl_genomes/test_variation.rb

@@ -0,0 +1,17 @@
+#
+# = test/unit/release_53/ensembl_genomes/test_variation.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'
+
+# TO BE DONE AS SOON AS ENSEMBL GENOMES VARIATIONS WILL BE RELEASED

data/test/unit/release_50/core/test_project.rb

@@ -0,0 +1,215 @@
+#
+# = test/unit/test_project.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2007
+#               Jan Aerts <http://jandot.myopenid.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
+
+DBConnection.connect('bos_taurus', 50)
+
+class CoordinateMappingsTestSimple < Test::Unit::TestCase
+  # First see if the relationships work
+  def test_assemblies
+    # Contig AAFC03055291 should only be a component of chromosome 20
+    contig_coord_system = CoordSystem.find_by_name('contig')
+    aafc03055291 = SeqRegion.find_by_name_and_coord_system_id('AAFC03055291', contig_coord_system.id)
+    assert_equal(1, aafc03055291.assembled_seq_regions.length)
+
+    # Chromosome 20 has 2970 components
+    chr_coord_system = CoordSystem.find_by_name('chromosome')
+    chr20 = SeqRegion.find_by_name_and_coord_system_id('20', chr_coord_system.id)
+    assert_equal(2970, chr20.component_seq_regions.length)
+
+    # Chromosome 20 has 2970 contigs
+    assert_equal(2970, chr20.component_seq_regions('contig').length)
+
+    # Positions of the link between Chr20 and AAFC03055291
+    # * Contig AAFC03055291 starts at position 13970982 on chromosome Chr20
+    assert_equal(13970982, aafc03055291.assembly_links_as_component(chr_coord_system)[0].asm_start)
+    end
+end
+
+class Sequences < Test::Unit::TestCase
+  def setup
+    @seq_region = SeqRegion.find(92594)
+  end
+
+  def test_simple
+    assert_equal('AGCTATTTTATGACTT', @seq_region.seq.slice(4,16))
+  end
+
+  def test_subseq
+    assert_equal('AGCTATTTTATGACTT', @seq_region.subseq(5,20))
+  end
+end
+
+#class SliceProjectFromComponentToAssembly < Test::Unit::TestCase
+#  # |------------------------------------------> chromosome
+#  #     ^                 ^
+#  #     |                 |
+#  #     |-----------------> scaffold
+#  def test_project_from_whole_component_to_assembly
+#    source_slice = Slice.fetch_by_region('contig','AAFC03055291')
+#    target_slices = source_slice.project('chromosome')
+#
+#    # Start and stop of chr4_105 on Chr4
+#    assert_equal(13970982, target_slices[0].start)
+#    assert_equal(13982069, target_slices[0].stop)
+#  end
+#
+#  # |------------------------------------------> chromosome
+#  #         ^        ^
+#  #         |        |
+#  #     |-----------------> scaffold
+#  def test_project_from_component_to_assembly_with_positions
+#    source_slice = Slice.fetch_by_region('scaffold','Chr4.003.105', 42, 2007)
+#    target_slices = source_slice.project('chromosome')
+#
+#    # Position 42 on chr4_105 is position 96652152, position 2007 is 96654117
+#    assert_equal(96652152, target_slices[0].start)
+#    assert_equal(96654117, target_slices[0].stop)
+#  end
+#
+#  # |------------------------------------------> scaffold
+#  #         ^        ^
+#  #         |        |
+#  #       ----------------> contig
+#  #      /
+#  #   |--
+#  def test_project_from_component_to_assembly_with_positions_and_cmp_start_not_1
+#    source_slice = Slice.fetch_by_region('contig', 'AAFC03020247', 42, 2007)
+#    target_slices = source_slice.project('scaffold')
+#
+#    # Position 42 on AAFC03020247 is position 6570 on ChrUn.003.3522, position 2007 is 8565
+#    assert_equal(6570, target_slices[0].start)
+#    assert_equal(8535, target_slices[0].stop)
+#  end
+#
+#  # |------------------------------------------> scaffold
+#  #         ^        ^
+#  #         |        |
+#  #     <-----------------| contig
+#  def test_project_from_component_to_assembly_with_strand
+#    source_slice_fw = Slice.fetch_by_region('contig', 'AAFC03020247')
+#    target_slices_fw = source_slice_fw.project('scaffold')
+#
+#    assert_equal(1, target_slices_fw[0].strand)
+#
+#    source_slice_rev = Slice.fetch_by_region('contig', 'AAFC03061502')
+#    target_slices_rev = source_slice_rev.project('scaffold')
+#
+#    assert_equal(-1, target_slices_rev[0].strand)
+#  end
+#end
+
+#class SliceProjectFromComponentToAssemblyUsingTopLevel < Test::Unit::TestCase
+#  # |------------------------------------------> chromosome
+#  #     ^                 ^
+#  #     |                 |
+#  #     |-----------------> scaffold
+#  def test_project_from_whole_component_to_assembly
+#    source_slice = Slice.fetch_by_region('scaffold','Chr4.003.105')
+#    target_slices = source_slice.project('toplevel')
+#
+#    # Start and stop of chr4_105 on Chr4
+#    assert_equal(96652111, target_slices[0].start)
+#    assert_equal(97251689, target_slices[0].stop)
+#  end
+#
+#  # |------------------------------------------> chromosome
+#  #         ^        ^
+#  #         |        |
+#  #     |-----------------> scaffold
+#  def test_project_from_component_to_assembly_with_positions
+#    source_slice = Slice.fetch_by_region('scaffold','Chr4.003.105', 42, 2007)
+#    target_slices = source_slice.project('toplevel')
+#
+#    # Position 42 on chr4_105 is position 96652152, position 2007 is 96654117
+#    assert_equal(96652152, target_slices[0].start)
+#    assert_equal(96654117, target_slices[0].stop)
+#  end
+#end
+
+class SliceProjectFromAssemblyToComponentForwardStrands < Test::Unit::TestCase
+  def setup
+    @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
+
+  #     |-----------------> 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_50/core/test_project_human.rb

@@ -0,0 +1,58 @@
+#
+# = test/unit/test_project.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2007
+#               Jan Aerts <http://jandot.myopenid.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
+
+DBConnection.connect('homo_sapiens', 50)
+
+class AssemblyExceptions < Test::Unit::TestCase
+  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

data/test/unit/release_50/core/test_relationships.rb

@@ -0,0 +1,66 @@
+#
+# = test/unit/test_transfers.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2007
+#               Jan Aerts <http://jandot.myopenid.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
+
+DBConnection.connect('homo_sapiens', 50)
+
+# Let's see if we can 'find' things
+class SimpleRecordsTest < Test::Unit::TestCase
+  def setup
+    @sry_gene = Gene.find(34927)
+    @sry_transcript = Transcript.find(60290)
+  end
+
+  def test_coord_system
+    coord_system = CoordSystem.find(17)
+    assert_equal('chromosome', coord_system.name)
+  end
+
+  def test_coord_system_toplevel
+    coord_system = CoordSystem.find(17).find_toplevel
+    assert_equal('chromosome', coord_system.name)
+  end
+
+  def test_coord_system_seqlevel
+    coord_system = CoordSystem.find(17).find_seqlevel
+    assert_equal('contig', coord_system.name)
+  end
+
+  def test_display_label
+    assert_equal('SRY', @sry_gene.display_label)
+    assert_equal('SRY', @sry_gene.display_name)
+    assert_equal('SRY', @sry_gene.label)
+    assert_equal('SRY', @sry_gene.name)
+
+    assert_equal('SRY-001', @sry_transcript.display_label)
+    assert_equal('SRY-001', @sry_transcript.display_name)
+    assert_equal('SRY-001', @sry_transcript.label)
+    assert_equal('SRY-001', @sry_transcript.name)
+  end
+end
+
+class RelationshipsTest < Test::Unit::TestCase
+  def test_go_terms
+    gene = Gene.find(34928)
+    assert_equal(["GO:0005576", "GO:0042742"], gene.go_terms.sort)
+  end
+  
+  def test_hgnc
+    gene = Gene.find_by_stable_id('ENSG00000169740')
+    assert_equal('ZNF32', gene.hgnc)
+  end
+end