[BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme test_analysis.rb, 1.8, 1.9

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv8138/test/unit/bio/util/restriction_enzyme

Modified Files:
	test_analysis.rb 
Log Message:
Bugfix

Index: test_analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_analysis.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** test_analysis.rb	5 Jan 2007 06:11:39 -0000	1.8
--- test_analysis.rb	28 Mar 2007 19:45:27 -0000	1.9
***************
*** 137,145 ****
      assert_equal(["ag", "cag"], Bio::Sequence::NA.new('cagagag').cut_with_enzymes('ag^ag', 'EcoRII').primary )
  
!     # NOTE: investigate where the '' is coming from
!     assert_equal(["", "ag", "ag", "cag", "ccagg"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag', 'EcoRII').primary )
    end
  
  end
  
! end
--- 137,172 ----
      assert_equal(["ag", "cag"], Bio::Sequence::NA.new('cagagag').cut_with_enzymes('ag^ag', 'EcoRII').primary )
  
!     # Note how EcoRII needs extra padding on the beginning and ending of the
!     # sequence 'ccagg' to make the match since the cut must occur between 
!     # two nucleotides and can not occur on the very end of the sequence.
!     #   
!     #   EcoRII:
!     #     :blunt: "0"
!     #     :c2: "5"
!     #     :c4: "0"
!     #     :c1: "-1"
!     #     :pattern: CCWGG
!     #     :len: "5"
!     #     :name: EcoRII
!     #     :c3: "0"
!     #     :ncuts: "2"
!     #   
!     #        -1 1 2 3 4 5
!     #   5' - n^c c w g g n - 3'
!     #   3' - n g g w c c^n - 5'
!     #   
!     #   (w == [at])
! 
!     assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag', 'EcoRII').primary )
!     assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag').primary )
!     assert_equal([], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('EcoRII').primary )
! 
!     assert_equal(["ag", "ag", "cag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag', 'EcoRII').primary )
!     assert_equal(["ag", "agccaggt", "cag"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag').primary )
!     assert_equal(["cagagag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('EcoRII').primary )
!     assert_equal(["a", "gtctctcggtcc"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('EcoRII').complement )  
    end
  
  end
  
! end
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