ruby-ensembl-api 0.9.6 → 1.0

data/test/unit/ensembl_genomes/test_gene.rb

@@ -1,52 +0,0 @@
-#
-# = 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

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

@@ -1,17 +0,0 @@
-#
-# = 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

@@ -1,215 +0,0 @@
-#
-# = 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

@@ -1,58 +0,0 @@
-#
-# = 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

@@ -1,66 +0,0 @@
-#
-# = 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