bio-ensembl 1.1.0

data/test/default/test_releases.rb

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+#
+# = test/unit/test_releases.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 TestRelease53 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_gene_stable_id_human
+    DBConnection.connect('homo_sapiens', 53)
+    slice = Slice.fetch_by_region('chromosome','1',1000,100000)
+    assert_equal(["ENSG00000146556","ENSG00000177693","ENSG00000197490","ENSG00000205292","ENSG00000219789","ENSG00000221311","ENSG00000222003","ENSG00000222027"], slice.genes.collect{|g| g.stable_id}.sort)
+  end
+end
+
+class TestRelease50 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+
+  def test_gene_stable_id
+    DBConnection.connect('homo_sapiens', 50)
+    slice = Slice.fetch_by_region('chromosome','1',1000,100000)
+    assert_equal(["ENSG00000146556", "ENSG00000177693", "ENSG00000197194", "ENSG00000197490", "ENSG00000205292", "ENSG00000219789", "ENSG00000221311"], slice.genes.collect{|g| g.stable_id}.sort)
+  end
+end
+
+class TestRelease49 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_slice_and_genes_mouse
+    DBConnection.connect('mus_musculus',49)
+    
+    slice = Slice.fetch_by_region('chromosome',"19",52571924,52572023)
+    assert_equal("AAGGTTGTATTCTAGTTTGCTCTCTGTTATTGTGACAAAGACAGGACCAAAGAAACTTGAGTAGGAAATGGTTGATAAAATCTTACAAGTTAGAAGGCAG",slice.seq.upcase)
+    
+    gene = Gene.find_by_stable_id("ENSMUSG00000017167")
+    assert_equal(101037431, gene.start)
+    assert_equal(101052034, gene.stop)
+    assert_equal(1,gene.transcripts.size)
+    assert_equal("ENSMUST00000103109",gene.transcripts[0].stable_id)
+  end
+  
+end
+
+class TestRelease47 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_slice_and_genes_mouse
+    DBConnection.connect('mus_musculus',47)
+    
+    slice = Slice.fetch_by_region('chromosome',"5",123840876,123912619)
+    genes = slice.genes
+    assert_equal("ENSMUSG00000038342",genes[0].stable_id)
+    slice = Slice.fetch_by_region('chromosome',"5",123840876,123840975)
+    assert_equal("TCTCAGTTCAGGTTCTATGGGGGGGAGGGGAGGGAATGAAAAGGATGTTAACAATCACCATCACCAGGGGGGACCAATTTGAAGATCTGATCGCCGGTGT",slice.seq.upcase)
+    
+    gene = Gene.find_by_stable_id("ENSMUSG00000017167")
+    assert_equal(101037431, gene.start)
+    assert_equal(101052034, gene.stop)
+    assert_equal(1,gene.transcripts.size)
+    assert_equal("ENSMUST00000103109",gene.transcripts[0].stable_id)
+  end
+  
+end
+
+class TestRelease45 < Test::Unit::TestCase
+
+  def teardown
+    DBConnection.remove_connection
+  end
+
+  def test_gene_stable_id_human
+    DBConnection.connect('homo_sapiens', 45)
+    slice = Slice.fetch_by_region('chromosome','1',1000,100000)
+    assert_equal(["ENSG00000146556", "ENSG00000177693", "ENSG00000197194", "ENSG00000197490", "ENSG00000205292"], slice.genes.collect{|g| g.stable_id}.sort)
+  end
+  
+  def test_slice_and_genes_mouse
+    DBConnection.connect('mus_musculus',45)
+    
+    slice = Slice.fetch_by_region('chromosome',"11",101037431,101037530)
+    assert_equal("ACTCTATCCAACTGAAACTGGAGATTAGTAACAGGGAAAAACAAACTCAACTGACAGCTGCTCCCAGTACAGTTCTTATGGTACAGGGAGCGTGGGAGTG",slice.seq.upcase)
+    
+    gene = Gene.find_by_stable_id("ENSMUSG00000017167")
+    assert_equal(100992131,gene.start)
+    assert_equal(101006814,gene.stop)
+    assert_equal("11",gene.seq_region.name)
+    assert_equal(2,gene.transcripts.size)
+  end
+  
+end
+ 
+class TestRelease37 < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+
+  def test_gene_stable_id_human
+    DBConnection.connect('homo_sapiens', 37)
+    slice = Slice.fetch_by_region('chromosome','1',1000,100000)
+    assert_equal(["ENSG00000146556", "ENSG00000177693", "ENSG00000197194", "ENSG00000197490"], slice.genes.collect{|g| g.stable_id}.sort)
+  end
+end
+ 
+
+
+
+
+

data/test/ensembl_genomes/test_collection.rb

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+#
+#
+# Copyright::   Copyright (C) 2011
+#               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 TestCollection < Test::Unit::TestCase
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_check_collection
+    DBConnection.ensemblgenomes_connect('bacillus_collection',8)
+    assert_equal(true,Collection.check)
+    DBConnection.connect('homo_sapiens',56)
+    assert_equal(false,Collection.check)
+  end
+  
+  def test_check_species
+    DBConnection.ensemblgenomes_connect('bacillus_collection',8)
+    assert_equal(["b_subtilis",
+     "b_amyloliquefaciens",
+     "b_anthracis_ames",
+     "b_anthracis_ames_ancestor",
+     "b_anthracis_sterne",
+     "b_cereus_atcc_10987",
+     "b_cereus_atcc_14579",
+     "b_cereus_cytotoxis",
+     "b_cereus_zk",
+     "b_clausii",
+     "b_halodurans",
+     "b_licheniformis_goettingen",
+     "b_licheniformis_novozymes",
+     "b_pumilus",
+     "b_thuringiensis",
+     "b_thuringiensis_konkukian",
+     "b_weihenstephanensis",
+     "b_cereus_ah820",
+     "b_cereus_ah187",
+     "b_cereus_03bb102",
+     "b_cereus_q1",
+     "b_cereus_g9842",
+     "b_cereus_b4264",
+     "b_anthracis_cdc_684",
+     "b_anthracis_a0248",
+     "b_thuringiensis_bt407",
+     "b_thuringiensis_ibl200",
+     "b_mycoides_rock1_4",
+     "b_thuringiensis_bgsc_4ba1_pondicheri",
+     "b_cereus_f65185",
+     "b_thuringiensis_bgsc_4bd1_huazhong",
+     "b_selenitireducens",
+     "b_cereus_r309803",
+     "b_cereus_bdrd_st196",
+     "b_thuringiensis_bgsc_4cc1_pulsiensis",
+     "b_cereus_95_8201",
+     "b_cereus_bdrd_st24",
+     "b_cereus_ah676",
+     "b_cereus_bdrd_st26",
+     "b_cereus_m1293",
+     "b_thuringiensis_atcc_10792",
+     "b_cereus_rock1_15",
+     "b_cereus_ah1273",
+     "b_thuringiensis_bgsc_4y1_tochigiensis",
+     "b_thuringiensis_t13001_pakistani",
+     "b_cereus_ah621",
+     "b_mycoides_dsm_2048",
+     "b_cereus_rock3_44",
+     "b_cereus_ah603",
+     "b_cereus_172560w",
+     "b_cereus_rock3_29",
+     "b_cereus_mm3",
+     "b_cereus_ah1272",
+     "b_pseudofirmus",
+     "b_cereus_rock4_18",
+     "b_thuringiensis_bgsc_4aw1_andalous",
+     "b_cereus_rock3_28",
+     "b_pseudomycoides",
+     "b_mycoides_rock3_17",
+     "b_thuringiensis_t01001",
+     "b_thuringiensis_t04001_sotto",
+     "b_cereus_bdrd_bcer4",
+     "b_thuringiensis_t03a001_kurstaki",
+     "b_thuringiensis_ibl4222",
+     "b_cereus_mm1550",
+     "b_cereus_bgsc_6e1",
+     "b_thuringiensis_bmb171",
+     "b_cereus_var_anthracis",
+     "b_cereus_atcc_10876",
+     "b_cereus_ah1271",
+     "b_cereus_atcc_4342",
+     "b_megaterium_atcc_12872",
+     "b_thuringiensis_bgsc_4aj1",
+     "b_cereus_rock4_2",
+     "b_cereus_rock3_42",
+     "b_cereus_rock1_3",
+     "b_tusciae",
+     "b_megaterium_dsm_319"],Collection.species)
+  end
+  
+  def test_get_species_id
+    DBConnection.ensemblgenomes_connect('bacillus_collection',8)
+    assert_equal(9,Collection.get_species_id("Bacillus cereus ZK"))
+    assert_nil(Collection.get_species_id("Dummy specie"))  
+  end
+  
+  def test_connection_with_a_species
+    assert_nothing_raised do 
+      DBConnection.ensemblgenomes_connect('b_licheniformis_goettingen',8)
+    end
+    assert_equal('b_licheniformis_goettingen', Ensembl::SESSION.collection_species)
+  end
+  
+end

data/test/ensembl_genomes/test_gene.rb

@@ -0,0 +1,46 @@
+#
+#
+# Copyright::   Copyright (C) 2011
+#               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 TestGene < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.ensemblgenomes_connect('pyrococcus_collection',8) 
+  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/ensembl_genomes/test_slice.rb

@@ -0,0 +1,65 @@
+#
+#
+# Copyright::   Copyright (C) 2011
+#               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 teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_fetch_by_region
+    DBConnection.ensemblgenomes_connect('mycobacterium_collection',8)
+    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',8)
+    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',8)
+    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('b_anthracis_Sterne',8)
+    slices = Slice.fetch_all('chromosome')
+    assert_equal(5228663,slices[0].length)
+  end
+  
+  def test_error_species
+    DBConnection.ensemblgenomes_connect('bacillus_collection',8)
+    assert_raise ArgumentError do 
+      Slice.fetch_by_region('chromosome',"Chromosome",831690,832175,1,"Wrong specie name")
+    end
+  end
+
+end

data/test/ensembl_genomes/test_variation.rb

@@ -0,0 +1,38 @@
+#
+#
+# Copyright::   Copyright (C) 2011
+#               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 TestVariation < Test::Unit::TestCase
+  
+  def setup
+    DBConnection.ensemblgenomes_connect('vitis_vinifera',8)
+  end
+  
+  def teardown
+    DBConnection.remove_connection
+  end
+  
+  def test_fetch_region
+    vf = Variation.find_by_name('ENSVVVI00603004').variation_features[0]
+    assert_equal(8789,vf.seq_region_start)
+    assert_equal(8789,vf.seq_region_end)
+    assert_equal('INTRONIC',vf.consequence_type)
+    assert_equal('T/A',vf.allele_string)
+    tv = vf.transcript_variations
+    t = tv[0].transcript
+    assert_equal("GSVIVT01004799001",t.stable_id)
+  end
+  
+  
+  
+  
+end

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-ensembl'
+
+class Test::Unit::TestCase
+end

data/test/release_50/core/test_project.rb

@@ -0,0 +1,210 @@
+#
+# = 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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+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