jandot-ruby-ensembl-api 0.9.2

data/test/unit/release_45/core/test_relationships.rb

@@ -0,0 +1,61 @@
+#
+# = 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 'ensembl'
+
+include Ensembl::Core
+
+DBConnection.connect('homo_sapiens')
+
+# Let's see if we can 'find' things
+class SimpleRecordsTest < Test::Unit::TestCase
+  def setup
+    @sry_gene = Gene.find(85743)
+    @sry_transcript = Transcript.find(271533)
+  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_toplevel
+    assert_equal('chromosome', coord_system.name)
+  end
+
+  def test_coord_system_seqlevel
+    coord_system = CoordSystem.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_HUMAN', @sry_transcript.display_label)
+    assert_equal('SRY_HUMAN', @sry_transcript.display_name)
+    assert_equal('SRY_HUMAN', @sry_transcript.label)
+    assert_equal('SRY_HUMAN', @sry_transcript.name)
+  end
+end
+
+class RelationshipsTest < Test::Unit::TestCase
+  def test_go_terms
+    gene = Gene.find(91283)
+    assert_equal(['GO:0000166','GO:0000287','GO:0003779','GO:0004674','GO:0005515','GO:0005524','GO:0005737','GO:0006468','GO:0007243','GO:0015629','GO:0016740','GO:0051128'], gene.go_terms.sort)
+  end
+end

data/test/unit/release_45/core/test_sequence.rb

@@ -0,0 +1,175 @@
+#
+# = test/unit/test_seq.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2007
+#               Jan Aerts <http://jandot.myopenid.com>
+# License::     Ruby's
+#
+# $Id:
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'yaml'
+require 'ensembl'
+
+include Ensembl::Core
+
+DBConnection.connect('homo_sapiens')
+
+class SequenceForSlice < Test::Unit::TestCase
+  def test_forward_strand_seqlevel
+    slice = Slice.new(SeqRegion.find(170931),5,15)
+    seq = 'gcagtggtgtg'
+    assert_equal(seq, slice.seq)
+  end
+
+  def test_reverse_strand_seqlevel
+    slice = Slice.new(SeqRegion.find(170931),5,15, -1)
+    seq = 'cacaccactgc'
+    assert_equal(seq, slice.seq)
+  end
+
+  def test_forward_strand_not_seqlevel_single_target
+    slice = Slice.new(SeqRegion.find(226044),69437100,69437110)
+    seq = 'gtctatttaca'
+    assert_equal(seq, slice.seq)
+  end
+
+  def test_reverse_strand_not_seqlevel_single_target
+    slice = Slice.new(SeqRegion.find(226044),69437100,69437110,-1)
+    seq = 'tgtaaatagac'
+    assert_equal(seq, slice.seq)
+  end
+
+  def test_forward_strand_not_seqlevel_composite_target
+    seq = ''
+    File.open('../../data/seq_forward_composite.fa').reject{|l| l=~/^>/}.each do |line|
+      line.chomp!
+      seq += line
+    end
+    seq.downcase!
+    slice = Slice.new(SeqRegion.find(226044),69387650,69487649)
+    assert_equal(seq, slice.seq)
+  end
+
+  def test_reverse_strand_not_seqlevel_composite_target
+    slice = Slice.new(SeqRegion.find(226044),69437061,69437160,-1)
+    assert_equal('nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgtaaatagacaactaacaagatagctgagattgtttccttatccagaca', slice.seq)
+  end
+
+end
+
+class SequenceForUnsplicedFeature < Test::Unit::TestCase
+  def test_forward_strand_seqlevel
+    marker_feature = MarkerFeature.find(1323757)
+    marker_seq = 'ggcttacttggaaaggtctcttccaacccaatattattcaaatactttcaattttcttctaatgtttttagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtggttttgttttatttcttttaattctctgatacatttagaatttcttttattattttattttattttattatttatttatttatttttgagacagagttttgctc'
+    assert_equal(marker_seq, marker_feature.seq)
+  end
+
+  def test_reverse_strand_seqlevel
+    gene = Gene.find_by_name('ANKRD56')
+
+    ankrd56_seq = 'atggcccgagagctgagccaggaggcactactggactttctgtgccaggctgggggccgcgtgaccaacgctgccttgctgagccacttcaagagctttctccgagaccccgacgcgtcccccagccagcaccagcaccgccgcgagctcttcaagggcttcgtcaactcggtcgccgcagtgcgccaggaccccgacggcaccaagtacgtggtgctcaagaggagatacagggaccttttgggggaggaggggctgcagcgaccccgcgagccgcccgcggccgcccccagtgcagggggagctgcgccctgctccccgcgaggcgcgcgccggggggagccgccccagcagcagcccaggcggcggcggcgcgagaaggagccggaggaggagccagcaggtgcagcagccagagccgccgacgcagcttgcaatggactcccgggcagcgactcccgtagggcgcccgggaagggcggcggatcgaagggcagtcccggacagaggccgccggtgcccgcagctgcagcggcaggggcccaggcgagagcgagctgcgcggcggcgaagacgcagggccgctgctgctgggaatgcctccagaacaacctggctgtactgccgggagagctcggcgcactcccgcactcggccaccgcggaggagaagccggcacgggctctgcctgcccaggatgaccgcggggcttccagggagcgggaagaaggcgcgctagctgagccggcgcctgtgcctgcagtggctcactcgcctcccgccaccgtcgaggctgcgacaagcagggcttccccgcctgctctcctgcccggccccgctccccgcggagaccggccggagctgctgacccccagctccctgcattattcgaccctgcagcagcagcagcagcgcactcgagagtgggtggccaggcacccgcaggtgcccgaggcccgtgatcagggccctatccgcgcctggtcggtgctgccagacaacttcctccagctgcccttggaacccggctccacggagcctaattcagagccgccagacccctgtctttcctcgcactctctctttcctgttgttccggatgagtcctgggaatcctgggcggggaacccttcattgactgtctttcgcagcattcgttgtcagctgtccctccaagatctggatgactttgtggaccaggagagtgatggcagtgaggagagcagcagtgggcccaaagactccccgggggcttctgaagaggggctgcaggttgtcttgggaaccccagatagggggaagctcaggaatccagctgggggcctttctgtatctcggaaggagggcagccccagccggagccctcagggtctcagaaacagaggggatggtcacatctctcagcaggtccctgcaggggctaatggccttgcaggccaccccctgaagcctttgccttggccagttcctaagttaaggaggtccctcaggaggagctctctggcagggagagccaaattgtcctcctctgatgaggagtacctcgatgagggcttgctgaaaagaagtcggcgcccacctcgatccaggaagccctccaaggcaggaacggcacccagcccaagggttgatgcaggtttatcactaaaacttgcagaggttaaggctgttgtggccgagcggggttggcgacacagcctgtgggtccccagtggggaggggtctgcagccttggccccccacagaacttctgagcacaaatcatccctggttccactagatgccagggagcatgagtggattgtgaagcttgccagtggctcctggattcaggtgtggactttgttctgggaggaccctcaactggccttgcacaaagactttttgactgggtacactgcgttgcactggatagccaaacatggtgacctcagggcccttcaggacttggtgtctggagcaaagaaggcagggattgtccttgatgtaaacgtgaggtccagttgtggatataccccgctgcaccttgcagccattcacggccaccagggggtcatcaaattgctagtgcaaaggttggcttctcgggtaaatgtcagggacagcagtgggaagaagccatggcagtatctaaccagtaatacctctggggaaatatggcagctgttgggagctcctcggggcaagcccattttccctgtctatcccttagttggaagttcttcccctaccagaaaggccaagagcaaggaaatatctagaagtgtcacccgaaaaacttccttcgctgcactactcaaaagtcagcacaacaagtggaaactggccaaccagtatgagaaattccacagtccaagggaaagagaagagtatagtgactga'
+    assert_equal(ankrd56_seq, gene.seq)
+  end
+
+  def test_reverse_strand_not_seqlevel
+    gene = Gene.find_by_name('DRD3')
+    drd3_gene_seq = ''
+    File.open('../../data/seq_drd3_gene.fa').reject{|l| l=~/^>/}.each do |line|
+      line.chomp!
+      drd3_gene_seq += line
+    end
+    drd3_gene_seq.downcase!
+    assert_equal(drd3_gene_seq, gene.seq)
+
+  end
+
+  def test_exon
+    exon = Exon.find(719588)
+    assert_equal('atggcatctctgagccagctgagtggccacctgaactacacctgtggggcagagaactccacaggtgccagccaggcccgcccacatgcctactatgccctctcctactgcgcgctcatcctggccatcgtcttcggcaatggcctggtgtgcatggctgtgctgaaggagcgggccctgcagactaccaccaactacttagtagtgagcctggctgtggcagacttgctggtggccaccttggtgatgccctgggtggtatacctggag', exon.seq)
+  end
+
+end
+
+class SequenceForSlicedFeature < Test::Unit::TestCase
+  def test_transcript_foward
+    transcript = Transcript.find(276333)
+    ub2r1_transcript_seq = ''
+    File.open('../../data/seq_ub2r1_transcript.fa').reject{|l| l=~/^>/}.each do |line|
+      line.chomp!
+      ub2r1_transcript_seq += line
+    end
+    ub2r1_transcript_seq.downcase!
+    assert_equal(ub2r1_transcript_seq, transcript.seq)
+
+  end
+
+  def test_transcript_reverse
+    transcript = Transcript.find(276225)
+    cso19_transcript_seq = ''
+    File.open('../../data/seq_cso19_transcript.fa').reject{|l| l=~/^>/}.each do |line|
+      line.chomp!
+      cso19_transcript_seq += line
+    end
+    cso19_transcript_seq.downcase!
+    assert_equal(cso19_transcript_seq, transcript.seq)
+  end
+
+end
+
+class SequenceForCDS < Test::Unit::TestCase
+  def setup
+    # Transcript tr_fw is ENST00000215574
+    @tr_fw = Transcript.find(276333)
+    # Transcript tr_rev is ENST00000315489
+    @tr_rev = Transcript.find(276225)
+  end
+
+  def test_cds_fw
+    ub2r1_coding_seq = ''
+    File.open('../../data/seq_ub2r1_coding.fa').reject{|l| l=~/^>/}.each do |line|
+      line.chomp!
+      ub2r1_coding_seq += line
+    end
+    ub2r1_coding_seq.downcase!
+    assert_equal(ub2r1_coding_seq, @tr_fw.cds_seq)
+  end
+
+  def test_cds_rev
+    cso19_coding_seq = ''
+    File.open('../../data/seq_cso19_coding.fa').reject{|l| l=~/^>/}.each do |line|
+      line.chomp!
+      cso19_coding_seq += line
+    end
+    cso19_coding_seq.downcase!
+    assert_equal(cso19_coding_seq, @tr_rev.cds_seq)
+  end
+
+  def test_five_prime_utr_fw
+    assert_equal('GGCAAGCGCCGGTGGGGCGGCGGCGCCAGAGCTGCTGGAGCGCTCGGGGTCCCCGGGCGGCGGCGGCGGCGCAGAGGAGGAGGCAGGCGGCGGCCCCGGTGGCTCCCCCCCGGACGGTGCGCGGCCCGGCCCGTCTCGCGAACTCGCGGTGGTCGCGCGGCCCCGCGCTGCTCCGACCCCGGGCCCCTCCGCCGCCGCC'.downcase, @tr_fw.five_prime_utr_seq)
+  end
+
+  def test_five_primer_utr_rev
+    assert_equal('ACTCGATCCCGGCCCCACTTCCAGGCCAGTGTCCGGCCGACCAGCCTGCCTTGGGCCAGGGCCCCACGACTCCCTGCTGCGGGACAAGAGGCCGTCTGTGCGGCTGTGGTCGTGGGAGGGTGTGGTGAGGCCGTGAAGGTGGGGACGGTGCCTGGGCCTGTGGCCGCCAGAGCTGCTGCGGCTCAGAAGGTAGCACCAGGCCCCGTGGGTGCTGTGGGGGCCATCGCCTGCCCACC'.downcase, @tr_rev.five_prime_utr_seq)
+  end
+
+  def test_three_prime_utr_fw
+    assert_equal('CACCACCAGAATAAACTTGCCGAGTTTACCTCACTAGGGCCGGACCCGTGGCTCCTTAGACGACAGACTACCTCACGGAGGTTTTGTGCTGGTCCCCGTCTCCTCTGGTTGTTTCGTTTTGGCTTTTTCTCCCTCCCCATGTCTGTTCTGGGTTTTCACGTGCTTCAGAGAAGAGGGGCTGCCCCACCGCCACTCACGTCACTCGGGGCTCGGTGGACGGGCCCAGGGTGGGAGCGGCCGGCCCACCTGTCCCCTCGGGAGGGGAGCTGAGCCCGACTTCTACCGGGGTCCCCCAGCTTCCGGACTGGCCGCACCCCGGAGGAGCCACGGGGGCGCTGCTGGGAACGTGGGCGGGGGGCCGTTTCCTGACACTACCAGCCTGGGAGGCCCAGGTGTAGCGGTCCGAGGGGCCCGGTCCTGCCTGTCAGCTCCAGGTCCTGGAGCCACGTCCAGCACAGAGTGGACGGATTCACCGTGGCCGACTCTTTTCCCTGCTTTGGTTTGTTTGAAATCTAAATAAAACTACTTTATG'.downcase, @tr_fw.three_prime_utr_seq)
+  end
+
+  def test_three_prime_utr_rev
+    assert_equal('GCCAGGCCTGTTTCCCACACAGTGAACGGGGGGCTGGCGGGCCTCTCCTGGGGCCTGGCTTTGGCTGGAGGGGCTAGAAGGCGAGAGGGGCTGGGAAAGGAGTCTTCCCTCCCCTTTCCTGAACTGTCCAGGTCCTTCTAGGACACCTGATCCTTCCAGTCCCTGGGGGCTGTGACCCATGGCCCTGTGCAGGGTGCAGGGTGAGTCTCCTTCCAGTGCCCCAGTTTCTTCCAGGTCACGCCAGGCCAGGCCAGGCCAGGTGGGGAAAGGGACACCTTCCGGCCCTCCCCAGTAGCTGGCTGGAGATGGAGCTTCCTGTGTCCCAGAACTCGGCGTCCAGCTCCACTAGGGCCTGGATCCCCATCACAGCTTGGGTTAGCCCCGGTCCCAGCCCAAACTCAGGCTGGAGGCAGCCCCGAGGCCTGTGCCTTTCCCACTCCACCTTCTACAGTTGCTTAGCCAATAAACCTTTCCTGGGCTGGAG'.downcase, @tr_rev.three_prime_utr_seq)
+  end
+
+  def test_protein_fw
+    assert_equal('MARPLVPSSQKALLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKARLKFPIDYPYSPPAFRFLTKMWHPNIYETGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPAPDEGSDLFYDDYYEDGEVEEEADSCFGDDEDDSGTEES*', @tr_fw.protein_seq)
+  end
+
+  def test_protein_rev
+    assert_equal('MGTLSCDSTPRLATAPLGRRVTEGQIPETGLRKSCGTATLENGSGPGLYVLPSTVGFINHDCTRVASPAYSLVRRPSEAPPQDTSPGPIYFLDPKVTRFGRSCTPAYSMQGRAKSRGPEVTPGPGAYSPEKVPPVRHRTPPAFTLGCRLPLKPLDTSAPAPNAYTMPPLWGSQIFTKPSSPSYTVVGRTPPARPPQDPAEIPGPGQYDSPDANTYRQRLPAFTMLGRPRAPRPLEETPGPGAHCPEQVTVNKARAPAFSMGIRHSKRASTMAATTPSRPAGHRLPGRCC*', @tr_rev.protein_seq)
+  end
+end
+

data/test/unit/release_45/core/test_slice.rb

@@ -0,0 +1,56 @@
+#
+# = 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')
+
+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
+    scaffold = SeqRegion.find_by_name('Chr4.003.122')
+    assert_equal(0, scaffold.simple_features.length)
+    assert_equal(122, scaffold.slice.simple_features.length)
+    slice = Slice.fetch_by_region('scaffold','Chr4.003.122')
+    assert_equal(122, slice.simple_features.length)
+  end
+end
+
+class SliceMethodMissing < Test::Unit::TestCase
+  def setup
+    @slice = Slice.new(SeqRegion.find_by_name('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(256, @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(34, @slice.transcripts.length)
+  end
+end

data/test/unit/release_45/core/test_transcript.rb

@@ -0,0 +1,94 @@
+#
+# = 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')
+
+class CodingPositions < Test::Unit::TestCase
+  def setup
+    # Transcript tr_fw is ENST00000215574
+    @tr_fw = Transcript.find(276333)
+    # Transcript tr_rev is ENST00000358041
+    @tr_rev = Transcript.find(276403)
+  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(276333)
+    # Transcript tr_rev is ENST00000315489
+    @tr_rev = Transcript.find(276225)
+  end
+  
+  def test_identify_exon
+    assert_equal(Exon.find(621287), @tr_fw.exon_for_cdna_position(601))
+    assert_equal(Exon.find(621287), @tr_fw.exon_for_genomic_position(488053))
+    assert_equal(Exon.find(620486), @tr_rev.exon_for_cdna_position(541))
+    assert_equal(Exon.find(620486), @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
+
+

data/test/unit/release_45/core/test_transform.rb

@@ -0,0 +1,223 @@
+#
+# = 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')
+
+# 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(2115)
+    target_gene = source_gene.transform('chromosome')
+
+    assert_equal('4', source_gene.seq_region.name)
+    assert_equal(1454668, source_gene.seq_region_start)
+    assert_equal(1483537, source_gene.seq_region_end)
+    assert_equal(1, source_gene.seq_region_strand)
+    assert_equal('4', target_gene.seq_region.name)
+    assert_equal(1454668, target_gene.seq_region_start)
+    assert_equal(1483537, 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(2408)
+    target_gene = source_gene.transform('chromosome')
+
+    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('4', target_gene.seq_region.name)
+    assert_equal(8104409, target_gene.seq_region_start)
+    assert_equal(8496477, 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