[BioRuby-cvs] bioruby/test/unit/bio test_alignment.rb,1.4,1.5

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory pub.open-bio.org:/tmp/cvs-serv24705/test/unit/bio

Modified Files:
	test_alignment.rb 
Log Message:
* consensus_iupac now returns only standard bases
'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v', 'h', 'd', 'b', 'n',
or nil (in SiteMethods#consensus_iupac) or '?' (or missing_char, in 
EnumerableExtension#consensus_iupac).
Note that consensus_iupac now does not return u and invalid letters
not defined in IUPAC standard even if all bases are equal.
* added more tests to test_alignment.rb



Index: test_alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_alignment.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** test_alignment.rb	25 Nov 2005 16:53:32 -0000	1.4
--- test_alignment.rb	2 Dec 2005 07:01:38 -0000	1.5
***************
*** 138,142 ****
    end #class TestAlignmentPropertyMethods
  
!   
    class TestAlignmentSite < Test::Unit::TestCase
  
--- 138,145 ----
    end #class TestAlignmentPropertyMethods
  
!   # This is a unit test of Bio::Alignment::Site class and
!   # Bio::Alignment::SiteMethods module.
!   # Since Bio::Alignment::Site includes Bio::Alignment::SiteMethods,
!   # we can test both at a time.
    class TestAlignmentSite < Test::Unit::TestCase
  
***************
*** 239,243 ****
--- 242,414 ----
    end #class TestAlignmentSite
  
+   class TestAlignmentSequenceArray < Test::Unit::TestCase
+     def test_each_seq
+       expected_results = [ 'atg', 'aag', 'acg' ]
+       a = Alignment::SequenceArray[ *expected_results ]
+       a.each_seq do |x|
+         assert_equal(expected_results.shift, x)
+       end
+       assert(expected_results.empty?)
+     end
+ 
+     def test_seqclass_default
+       a = Alignment::SequenceArray.new
+       assert_equal(String, a.seqclass)
+     end
+ 
+     def test_seqclass
+       a = Alignment::SequenceArray[ Bio::Sequence::NA.new('atg') ]
+       assert_equal(Bio::Sequence::NA, a.seqclass)
+     end
+ 
+     def test_seqclass=()
+       a = Alignment::SequenceArray.new
+       assert_equal(String, a.seqclass)
+       a << Bio::Sequence::NA.new('a')
+       assert_equal(Bio::Sequence::NA, a.seqclass)
+       a.seqclass = Bio::Sequence::AA
+       assert_equal(Bio::Sequence::AA, a.seqclass)
+     end
+ 
+     def test_alignment_length
+       a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+       assert_equal(4, a.alignment_length)
+     end
+ 
+     def test_private_alignment_site
+       a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+       assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
+                    a.instance_eval { _alignment_site(1) })
+     end
  
+     def test_alignment_site
+       a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+       assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
+                    a.__send__(:_alignment_site, 1))
+     end
+ 
+     def test_each_site
+       expected_results = [
+         Alignment::Site[ 'a', 'a', 'a', 'a', '-' ],
+         Alignment::Site[ '-', 't', 't', 't', '-' ],
+         Alignment::Site[ '-', '-', 'g', 'g', '-' ],
+         Alignment::Site[ '-', '-', 'c', '-', '-' ]
+       ]
+       a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+       a.each_site do |site|
+         assert_equal(expected_results.shift, site)
+       end
+       assert(expected_results.empty?)
+     end
+ 
+     def test_each_site_step
+       expected_results = [
+         Alignment::Site[ '-', 't', 't', 't', '-' ], # site 1
+         Alignment::Site[ '-', 'a', 'g', 't', '-' ], # site 3
+       ]
+       a = Alignment::SequenceArray[ 'a', 'atgatc', 'atggcc', 'atgtga', '' ]
+       a.each_site_step(1, 4, 2) do |site|
+         assert_equal(expected_results.shift, site)
+       end
+       assert(expected_results.empty?)
+     end
+ 
+     def test_alignment_collect
+       a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+       assert_equal(Alignment::SequenceArray[ 'a', 'au', 'augc', 'aug', '' ],
+                    a.alignment_collect { |x| x.gsub(/t/, 'u') })
+     end
+ 
+     def test_alignment_window
+       a = Alignment::SequenceArray[ 'a', 'at', 'atgca', 'atg', '' ]
+       assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', '' ],
+                    a.alignment_window(1, 3))
+     end
+ 
+     def test_each_window
+       expected_results = [
+         Alignment::SequenceArray[ 'atg', 'tcg', '' ], # 0..2
+         Alignment::SequenceArray[ 'gca', 'gat', '' ], # 2..4
+         Alignment::SequenceArray[ 'atg', 'tgc', '' ], # 4..6
+         Alignment::SequenceArray[ 'c', 'a', '' ]      # 7..7
+       ]
+       a = Alignment::SequenceArray[ 'atgcatgc', 'tcgatgca', '' ]
+       r = a.each_window(3, 2) do |x|
+         assert_equal(expected_results.shift, x)
+       end
+       assert_equal(expected_results.shift, r)
+       assert(expected_results.empty?)
+     end
+ 
+     def test_collect_each_site
+       a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+       assert_equal(["aaaa-", "-ttt-", "--gg-", "--c--" ],
+                    a.collect_each_site { |x| x.join('') })
+     end
+ 
+     def test_consensus_each_site_default
+       expected_results = [
+         Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ],
+         Alignment::Site[ 'a', 'c', 'g', 't', '-' ]
+       ]
+ 
+       a = Alignment::SequenceArray[ 'aa', 'ac', 'ag', 'at', 'a-' ]
+       result = a.consensus_each_site do |site|
+         assert_equal(expected_results.shift, site)
+         'x'
+       end
+       assert_equal('xx', result)
+       assert(expected_results.empty?)
+     end
+ 
+     def test_consensus_each_site_gap_mode_1
+       expected_results = [
+         Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ]
+       ]
+ 
+       a = Alignment::SequenceArray[ 'aa', 'ac', 'ag', 'at', 'a-' ]
+       result = a.consensus_each_site(:gap_mode => 1) do |site|
+         assert_equal(expected_results.shift, site)
+         'x'
+       end
+       assert_equal('x-', result)
+       assert(expected_results.empty?)
+     end
+ 
+     def test_consensus_each_site_gap_mode_minus1
+       expected_results = [
+         Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ],
+         Alignment::Site[ 'a', 'c', 'g', 't' ]
+       ]
+ 
+       a = Alignment::SequenceArray[ 'aa', 'ac', 'ag', 'at', 'a-' ]
+       result = a.consensus_each_site(:gap_mode => -1) do |site|
+         assert_equal(expected_results.shift, site)
+         'x'
+       end
+       assert_equal('xx', result)
+       assert(expected_results.empty?)
+     end
+ 
+     def test_consensus_string_default
+       a = Alignment::SequenceArray[ 'ata', 'aac', 'aag', 'aat' ]
+       assert_equal('a??', a.consensus_string)
+     end
+ 
+     def test_consensus_string_half
+       a = Alignment::SequenceArray[ 'ata', 'aac', 'aag', 'aat' ]
+       assert_equal('aa?', a.consensus_string(0.5))
+     end
+ 
+     def test_consensus_iupac
+       a = Alignment::SequenceArray[
+         'acgtaaaccgaaacaz',
+         'acgtaaaccgccggcz',
+         'acgtcgtgttgtttgz',
+         'acgtcgtgttaaactz' ]
+       assert_equal('acgtmrwsykvhdbn?', a.consensus_iupac)
+     end
+ 
+   end #class TestAlignmentSequenceArray