ruby-ensembl-api 0.9.6 → 1.0

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

@@ -1,175 +0,0 @@
-#
-# = test/unit/test_seq.rb - Unit test for Ensembl::Core
-#
-# Copyright::   Copyright (C) 2007
-#               Jan Aerts <http://jandot.myopenid.com>
-# License::     Ruby's
-#
-# $Id:
-require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
-
-require 'test/unit'
-require 'yaml'
-require 'lib/ensembl'
-
-include Ensembl::Core
-
-DBConnection.connect('homo_sapiens', 50)
-
-#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(73491) # UB2R1 = CDC34
-    ub2r1_transcript_seq = ''
-    File.open('test/unit/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(107548)
-    rnd3_transcript_seq = ''
-    File.open('test/unit/data/seq_rnd3_transcript.fa').reject{|l| l=~/^>/}.each do |line|
-      line.chomp!
-      rnd3_transcript_seq += line
-    end
-    rnd3_transcript_seq.downcase!
-    assert_equal(rnd3_transcript_seq, transcript.seq)
-  end
-
-end
-
-class SequenceForCDS < 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_cds_fw
-    ub2r1_coding_seq = ''
-    File.open('test/unit/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('test/unit/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_50/core/test_slice.rb

@@ -1,121 +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 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

@@ -1,108 +0,0 @@
-#
-# = 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 'lib/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

@@ -1,223 +0,0 @@
-#
-# = 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 'lib/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