jandot-ruby-ensembl-api 0.9.2

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

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+#
+# = 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 'ensembl'
+
+include Ensembl::Core
+DBConnection.connect('bos_taurus', 50)
+
+class GetFeatures < Test::Unit::TestCase
+  # Chr4.003.122 has no simple features in itself, but the corresponding region
+  # covered by the chromosome has 37. In addition, contigs within the scaffold
+  # have 85. Total should therefore be 122.
+  def test_simple_features
+    contig = SeqRegion.find_by_name('AAFC03055312')
+    assert_equal(19, contig.simple_features.length)
+    assert_equal(19, contig.slice.simple_features.length)
+    slice = Slice.fetch_by_region('contig','AAFC03055312')
+    assert_equal(19, slice.simple_features.length)
+  end
+end
+
+class SliceMethodMissing < Test::Unit::TestCase
+  def setup
+    @slice = Slice.fetch_by_region('chromosome','4',10000,10000000)
+  end
+  
+  # There is not NotExistingTable class
+  def test_non_existing_tables
+    assert_raise(NoMethodError) { @slice.not_existing_tables }
+  end
+  
+  # A slice can get its exons
+  def test_exons
+    assert_equal(291, @slice.exons.length)
+    assert_equal(Exon, @slice.exons[0].class)
+  end
+  
+  # A slice can _not_ get its markers; it has marker_features instead.
+  def test_markers
+    assert_raise(NoMethodError) { @slice.markers }
+  end
+  
+  def test_transcripts
+    assert_equal(36, @slice.transcripts.length)
+  end
+end
+
+class GetOverlappingObjects < Test::Unit::TestCase
+  def setup
+    @small_slice = Slice.fetch_by_region('chromosome','Un.004.10515',850,900)
+    @genes_inclusive = @small_slice.genes(true)
+    @genes_exclusive = @small_slice.genes
+    
+    @large_slice = Slice.fetch_by_region('contig','AAFC03055312',1,18210)
+    @repeats_inclusive = @large_slice.repeat_features(true).select{|r| r.analysis_id == 6}
+  end
+  
+  def test_get_gene
+    assert_equal(1, @genes_inclusive.length)
+    assert_equal('ENSBTAG00000039669', @genes_inclusive[0].stable_id)
+    assert_equal(0, @genes_exclusive.length)
+  end
+  
+  def test_get_repeat_features
+    assert_equal(2, @repeats_inclusive.length)
+  end
+end
+
+class ExcisingSlice < Test::Unit::TestCase
+  def setup
+    @original_slice = Slice.fetch_by_region('chromosome','1',1,1000)
+  end
+  
+  def test_excise_one_range
+    output = @original_slice.excise([20..50])
+    assert_equal(2, output.length)
+    assert_equal('chromosome:Btau_4.0:1:1:19:1', output[0].to_s)
+    assert_equal('chromosome:Btau_4.0:1:51:1000:1', output[1].to_s)
+  end
+  
+  def test_excise_two_nonoverlapping_ranges
+    output = @original_slice.excise([20..50,100..200])
+    assert_equal(3, output.length)
+    assert_equal('chromosome:Btau_4.0:1:1:19:1', output[0].to_s)
+    assert_equal('chromosome:Btau_4.0:1:51:99:1', output[1].to_s)
+    assert_equal('chromosome:Btau_4.0:1:201:1000:1', output[2].to_s)
+  end
+
+  def test_excise_two_overlapping_ranges
+    output = @original_slice.excise([20..150,100..200])
+    assert_equal(2, output.length)
+    assert_equal('chromosome:Btau_4.0:1:1:19:1', output[0].to_s)
+    assert_equal('chromosome:Btau_4.0:1:201:1000:1', output[1].to_s)
+  end
+
+  def test_excise_two_adjacent_ranges
+    output = @original_slice.excise([20..99,100..200])
+    assert_equal(2, output.length)
+    assert_equal('chromosome:Btau_4.0:1:1:19:1', output[0].to_s)
+    assert_equal('chromosome:Btau_4.0:1:201:1000:1', output[1].to_s)
+  end
+  
+  def test_excise_internal_ranges
+    output = @original_slice.excise([20..300,100..200])
+    assert_equal(2, output.length)
+    assert_equal('chromosome:Btau_4.0:1:1:19:1', output[0].to_s)
+    assert_equal('chromosome:Btau_4.0:1:201:1000:1', output[1].to_s)
+  end
+
+  
+end

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

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+#
+# = test/unit/test_transcript.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 'ensembl'
+
+include Ensembl::Core
+
+DBConnection.connect('homo_sapiens', 50)
+
+class CodingPositions < Test::Unit::TestCase
+  def setup
+    # Transcript tr_fw is ENST00000215574
+    @tr_fw = Transcript.find(73491)
+    # Transcript tr_rev is ENST00000358041
+    @tr_rev = Transcript.find(73774)
+  end
+
+  def test_transcript_coords
+    assert_equal(482733, @tr_fw.seq_region_start)
+    assert_equal(493084, @tr_fw.seq_region_end)
+    assert_equal(595371, @tr_rev.seq_region_start)
+    assert_equal(598309, @tr_rev.seq_region_end)
+  end
+
+  def test_coding_regions_genomic_coords_of_fw
+    assert_equal(482932, @tr_fw.coding_region_genomic_start)
+    assert_equal(492552, @tr_fw.coding_region_genomic_end)
+  end
+
+  def test_coding_regions_genomic_coords_of_rev
+    assert_equal(597652, @tr_rev.coding_region_genomic_start)
+    assert_equal(598047, @tr_rev.coding_region_genomic_end)
+  end
+  
+  def test_coding_regions_cdna_coords_of_fw
+    assert_equal(200, @tr_fw.coding_region_cdna_start)
+    assert_equal(910, @tr_fw.coding_region_cdna_end)
+  end
+
+  def test_coding_regions_cdna_coords_of_rev
+    assert_equal(263, @tr_rev.coding_region_cdna_start)
+    assert_equal(658, @tr_rev.coding_region_cdna_end)
+  end
+  
+end
+
+class GenomicVsCDna < Test::Unit::TestCase
+  def setup
+    # Transcript tr_fw is ENST00000215574
+    @tr_fw = Transcript.find(73491)
+    # Transcript tr_rev is ENST00000315489
+    @tr_rev = Transcript.find(73411)
+  end
+  
+  def test_identify_exon
+    assert_equal(Exon.find(374767), @tr_fw.exon_for_cdna_position(601))
+    assert_equal(Exon.find(374767), @tr_fw.exon_for_genomic_position(488053))
+    assert_equal(Exon.find(374458), @tr_rev.exon_for_cdna_position(541))
+    assert_equal(Exon.find(374458), @tr_rev.exon_for_genomic_position(418719))
+  end
+  
+  def test_cdna2genomic
+    assert_equal(488053, @tr_fw.cdna2genomic(601))
+    assert_equal(418719, @tr_rev.cdna2genomic(541))
+  end
+  
+  def test_cds2genomic
+    assert_equal(488053, @tr_fw.cds2genomic(401))
+    assert_equal(418719, @tr_rev.cds2genomic(304))
+  end
+  
+  def test_genomic2cdna
+    assert_equal(601, @tr_fw.genomic2cdna(488053))
+    assert_equal(541, @tr_rev.genomic2cdna(418719))
+  end
+  
+  def test_genomic2cds
+    assert_equal(401, @tr_fw.genomic2cds(488053))
+    assert_equal(304, @tr_rev.genomic2cds(418719))
+  end
+end
+
+class TestIntron < Test::Unit::TestCase
+  def setup
+    @transcript = Transcript.find(58973)
+    @introns = @transcript.introns
+  end
+  
+  def test_get_introns
+    assert_equal(2, @introns.length)
+  end
+  
+  def test_intron_slices
+    assert_equal('chromosome:NCBI36:8:159418:172128:-1', @introns[0].slice.to_s)
+  end
+end
+

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

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+#
+# = test/unit/test_transform.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 'ensembl'
+
+include Ensembl::Core
+DBConnection.connect('bos_taurus', 50)
+
+# 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
+  # |-------|========>-------------------------> chromosome
+  #         ^        ^
+  #         |        |
+  # |-------|========>-------------------------> chromosome
+  # This should return itself.
+  def test_fw
+    source_gene = Gene.find(6043)
+    target_gene = source_gene.transform('chromosome')
+
+    assert_equal('4', source_gene.seq_region.name)
+    assert_equal(4595538, source_gene.seq_region_start)
+    assert_equal(4827723, source_gene.seq_region_end)
+    assert_equal(1, source_gene.seq_region_strand)
+    assert_equal('4', target_gene.seq_region.name)
+    assert_equal(4595538, target_gene.seq_region_start)
+    assert_equal(4827723, target_gene.seq_region_end)
+    assert_equal(1, target_gene.seq_region_strand)
+  end
+
+  # |-------<========|-------------------------> chromosome
+  #         ^        ^
+  #         |        |
+  # |-------<========|-------------------------> chromosome
+  # This should return itself.
+  def test_rev
+    source_gene = Gene.find(6053)
+    target_gene = source_gene.transform('chromosome')
+
+    assert_equal('4', source_gene.seq_region.name)
+    assert_equal(5199677, source_gene.seq_region_start)
+    assert_equal(5201728, source_gene.seq_region_end)
+    assert_equal(-1, source_gene.seq_region_strand)
+    assert_equal('4', target_gene.seq_region.name)
+    assert_equal(5199677, target_gene.seq_region_start)
+    assert_equal(5201728, target_gene.seq_region_end)
+    assert_equal(-1, target_gene.seq_region_strand)
+  end
+end
+
+## Test names refer to:
+## (1) direction of gene vs chromosome
+## (2) direction of component (scaffold) vs assembly (chromosome)
+#class TransformFromComponentToAssembly < Test::Unit::TestCase
+#  def test_fw_fw
+#    assert true
+#  end
+#
+#  def test_fw_rev
+#    assert true
+#  end
+#
+#  def test_rev_fw
+#    assert true
+#  end
+#
+#  def test_rev_rev
+#    assert true
+#  end
+#end
+#
+## Test names refer to:
+## (1) direction of gene vs chromosome
+## (2) direction of component (scaffold) vs assembly (chromosome)
+## We have to test for features that are covered by a scaffold, and those
+## overlapping more than 1 scaffold.
+#class TransformFromAssemblyToComponent < Test::Unit::TestCase
+#  #       |-----------------> scaffold
+#  #           ^     ^
+#  #           |     |
+#  # |---------|=====>-----------------------------> chromosome
+#  def test_fw_fw_full_overlap
+#    source_gene = Gene.find(2995)
+#    target_gene = source_gene.transform('scaffold')
+#
+#    assert_equal('4', source_gene.seq_region.name)
+#    assert_equal(10333321, source_gene.seq_region_start)
+#    assert_equal(10510842, source_gene.seq_region_end)
+#    assert_equal(1, source_gene.seq_region_strand)
+#    assert_equal('Chr4.003.12', target_gene.seq_region.name)
+#    assert_equal(43842, target_gene.seq_region_start)
+#    assert_equal(221363, target_gene.seq_region_end)
+#    assert_equal(1, target_gene.seq_region_strand)
+#  end
+#
+#  #       |-----------------> scaffold
+#  #       |
+#  #       |
+#  # |---|===>-------------------------------> chromosome
+#  def test_fw_fw_partial_overlap
+#    source_feature = PredictionTranscript.find(52425)
+#    target_feature = source_feature.transform('scaffold')
+#
+#    assert_equal('4', source_feature.seq_region.name)
+#    assert_equal(1443280, source_feature.seq_region_start)
+#    assert_equal(1482777, source_feature.seq_region_end)
+#    assert_equal(1, source_feature.seq_region_strand)
+#    assert_equal(nil, target_feature)
+#  end
+#
+#  #       <-----------------| scaffold
+#  #            ^     ^
+#  #            |     |
+#  # |----------|=====>-----------------------------> chromosome
+#  def test_fw_rev_full_overlap
+#    source_gene = Gene.find(2708)
+#    target_gene = source_gene.transform('scaffold')
+#
+#    assert_equal('4', source_gene.seq_region.name)
+#    assert_equal(8312492, source_gene.seq_region_start)
+#    assert_equal(8312812, source_gene.seq_region_end)
+#    assert_equal(1, source_gene.seq_region_strand)
+#    assert_equal('Chr4.003.10', target_gene.seq_region.name)
+#    assert_equal(1774466, target_gene.seq_region_start)
+#    assert_equal(1774786, target_gene.seq_region_end)
+#    assert_equal(-1, target_gene.seq_region_strand)
+#  end
+#
+#  #       <-----------------| scaffold
+#  #                         |
+#  #                         |
+#  # |---------------------|===>------------------> chromosome
+#  def test_fw_rev_partial_overlap
+#    source_feature = PredictionTranscript.find(23305)
+#    target_feature = source_feature.transform('scaffold')
+#
+#    assert_equal('4', source_feature.seq_region.name)
+#    assert_equal(10008188, source_feature.seq_region_start)
+#    assert_equal(10156104, source_feature.seq_region_end)
+#    assert_equal(1, source_feature.seq_region_strand)
+#    assert_equal(nil, target_feature)
+#  end
+#
+#  #       |-----------------> scaffold
+#  #       |    ^     ^
+#  #       |    |     |
+#  # |---<===|--<=====|-----------------------------> chromosome
+#  def test_rev_fw_full_overlap
+#    source_gene = Gene.find(3124)
+#    target_gene = source_gene.transform('scaffold')
+#
+#    assert_equal('4', source_gene.seq_region.name)
+#    assert_equal(10353230, source_gene.seq_region_start)
+#    assert_equal(10371155, source_gene.seq_region_end)
+#    assert_equal(-1, source_gene.seq_region_strand)
+#    assert_equal('Chr4.003.12', target_gene.seq_region.name)
+#    assert_equal(63751, target_gene.seq_region_start)
+#    assert_equal(81676, target_gene.seq_region_end)
+#    assert_equal(-1, target_gene.seq_region_strand)
+#  end
+#
+#  #       |-----------------> scaffold
+#  #                         |
+#  #                         |
+#  # |---------------------<===|------------------> chromosome
+#  def test_rev_fw_partial_overlap
+#    source_feature = PredictionTranscript.find(24185)
+#    target_feature = source_feature.transform('scaffold')
+#
+#    assert_equal('4', source_feature.seq_region.name)
+#    assert_equal(11389212, source_feature.seq_region_start)
+#    assert_equal(11471635, source_feature.seq_region_end)
+#    assert_equal(-1, source_feature.seq_region_strand)
+#    assert_equal(nil, target_feature)
+#  end
+#
+#  #       <-----------------| scaffold
+#  #       |    ^     ^
+#  #       |    |     |
+#  # |---<===|--<=====|-----------------------------> chromosome
+#  def test_rev_rev_full_overlap
+#    source_gene = Gene.find(2408)
+#    target_gene = source_gene.transform('scaffold')
+#
+#    assert_equal('4', source_gene.seq_region.name)
+#    assert_equal(8104409, source_gene.seq_region_start)
+#    assert_equal(8496477, source_gene.seq_region_end)
+#    assert_equal(-1, source_gene.seq_region_strand)
+#    assert_equal('Chr4.003.10', target_gene.seq_region.name)
+#    assert_equal(1590801, target_gene.seq_region_start)
+#    assert_equal(1982869, target_gene.seq_region_end)
+#    assert_equal(1, target_gene.seq_region_strand)
+#  end
+#
+#  #       <-----------------| scaffold
+#  #       |
+#  #       |
+#  # |---<===|-----------------------------> chromosome
+#  def test_rev_rev_partial_overlap
+#    source_feature = Transcript.find(14723)
+#    target_feature = source_feature.transform('scaffold')
+#
+#    assert_equal('4', source_feature.seq_region.name)
+#    assert_equal(55713316, source_feature.seq_region_start)
+#    assert_equal(55792273, source_feature.seq_region_end)
+#    assert_equal(-1, source_feature.seq_region_strand)
+#    assert_equal(nil, target_feature)
+#  end
+#
+#end