bio-ensembl 1.1.0

data/test/release_50/core/test_project_human.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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+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/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/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/release_50/core/test_relationships.rb

@@ -0,0 +1,72 @@
+#
+# = 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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+
+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
+
+class ReflectionTest < Test::Unit::TestCase
+  def test_has_what
+    assert_equal(Gene.has_what.sort.join(';'), 'attrib_types;gene_attribs;gene_stable_id;object_xrefs;transcripts;xrefs')
+  end
+  
+  def test_belongs_to_what
+    assert_equal(Gene.belongs_to_what.sort.join(';'), 'analysis;seq_region')
+  end
+end
+

data/test/release_50/core/test_sequence.rb

@@ -0,0 +1,170 @@
+#
+# = 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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+
+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/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/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/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/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/release_50/core/test_slice.rb

@@ -0,0 +1,116 @@
+#
+# = 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 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/release_50/core/test_transcript.rb

@@ -0,0 +1,125 @@
+#
+# = 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 File.expand_path File.join(File.dirname(__FILE__),"../../helper.rb")
+
+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
+  #From BioMart. Columns:
+  #  Ensembl_Transcript_ID
+  #  Chromosome
+  #  Gene_Start
+  #  Gene_End
+  #  Transcript_Start
+  #  Transcript_End
+  #  Strand
+  #  Gene
+  #  Exon_Chr_Start
+  #  Exon_Chr_End
+  #  Exon_Rank_in_Transcript
+  #  phase
+  #ENST00000215574	19	482733	493084	482733	493084	1	CDC34	482733	483108	1	-1
+  #ENST00000215574	19	482733	493084	482733	493084	1	CDC34	486837	486923	2	0
+  #ENST00000215574	19	482733	493084	482733	493084	1	CDC34	487243	487340	3	0
+  #ENST00000215574	19	482733	493084	482733	493084	1	CDC34	488013	488147	4	2
+  #ENST00000215574	19	482733	493084	482733	493084	1	CDC34	492339	493084	5	2
+  #
+  #ENST00000315489	19	414360	425983	414360	425983	-1	C19orf19	425621	425983	1	-1
+  #ENST00000315489	19	414360	425983	414360	425983	-1	C19orf19	423394	423501	2	1
+  #ENST00000315489	19	414360	425983	414360	425983	-1	C19orf19	418649	418762	3	1
+  #ENST00000315489	19	414360	425983	414360	425983	-1	C19orf19	414360	415364	4	1
+  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(488052, @tr_fw.cdna2genomic(601))
+    assert_equal(418693, @tr_rev.cdna2genomic(541))
+  end
+  
+  def test_cds2genomic
+    assert_equal(488052, @tr_fw.cds2genomic(401))
+    assert_equal(418693, @tr_rev.cds2genomic(304))
+  end
+  
+  def test_genomic2cdna
+    assert_equal(601, @tr_fw.genomic2cdna(488052))
+    assert_equal(541, @tr_rev.genomic2cdna(418693))
+  end
+  
+  def test_genomic2cds
+    assert_equal(401, @tr_fw.genomic2cds(488052))
+    assert_equal(304, @tr_rev.genomic2cds(418693))
+  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
+