code_ruby/test/maasha/seq/test_trim.rb

   1 #!/usr/bin/env ruby
   2
   3 require 'maasha/seq'
   4 require 'test/unit'
   5 require 'pp'
   6
   7 class TestTrim < Test::Unit::TestCase
   8   def setup
   9     @entry = Seq.new
  10   end
  11
  12   def test_Trim_quality_trim_with_missing_seq_raises
  13     @entry.qual = "hhhh"
  14     assert_raise(TrimError) { @entry.quality_trim_right(20) }
  15     assert_raise(TrimError) { @entry.quality_trim_right!(20) }
  16     assert_raise(TrimError) { @entry.quality_trim_left(20) }
  17     assert_raise(TrimError) { @entry.quality_trim_left!(20) }
  18     assert_raise(TrimError) { @entry.quality_trim(20) }
  19     assert_raise(TrimError) { @entry.quality_trim!(20) }
  20   end
  21
  22   def test_Trim_quality_trim_with_missing_qual_raises
  23     @entry.seq = "ATCG"
  24     assert_raise(TrimError) { @entry.quality_trim_right(20) }
  25     assert_raise(TrimError) { @entry.quality_trim_right!(20) }
  26     assert_raise(TrimError) { @entry.quality_trim_left(20) }
  27     assert_raise(TrimError) { @entry.quality_trim_left!(20) }
  28     assert_raise(TrimError) { @entry.quality_trim(20) }
  29     assert_raise(TrimError) { @entry.quality_trim!(20) }
  30   end
  31
  32   def test_Trim_quality_trim_with_bad_min_raises
  33     @entry.seq  = "ATCG"
  34     @entry.qual = "hhhh"
  35
  36     [-1, 41].each do |min|
  37       assert_raise(TrimError) { @entry.quality_trim_right(min) }
  38       assert_raise(TrimError) { @entry.quality_trim_right!(min) }
  39       assert_raise(TrimError) { @entry.quality_trim_left(min) }
  40       assert_raise(TrimError) { @entry.quality_trim_left!(min) }
  41       assert_raise(TrimError) { @entry.quality_trim(min) }
  42       assert_raise(TrimError) { @entry.quality_trim!(min) }
  43     end
  44   end
  45
  46   def test_Trim_quality_trim_with_ok_min_dont_raise
  47     @entry.seq  = "ATCG"
  48     @entry.qual = "hhhh"
  49
  50     [0, 40].each do |min|
  51       assert_nothing_raised { @entry.quality_trim_right(min) }
  52       assert_nothing_raised { @entry.quality_trim_right!(min) }
  53       assert_nothing_raised { @entry.quality_trim_left(min) }
  54       assert_nothing_raised { @entry.quality_trim_left!(min) }
  55       assert_nothing_raised { @entry.quality_trim(min) }
  56       assert_nothing_raised { @entry.quality_trim!(min) }
  57     end
  58   end
  59
  60   def test_Trim_quality_trim_right_returns_correctly
  61     @entry.seq  = "AAAAATCG"
  62     @entry.qual = "hhhhhgfe"
  63     new_entry = @entry.quality_trim_right(38)
  64     assert_equal("AAAAATC", new_entry.seq)
  65     assert_equal("hhhhhgf", new_entry.qual)
  66     assert_equal("AAAAATCG", @entry.seq)
  67     assert_equal("hhhhhgfe", @entry.qual)
  68   end
  69
  70   def test_Trim_quality_trim_right_bang_returns_correctly
  71     @entry.seq  = "AAAAATCG"
  72     @entry.qual = "hhhhhgfe"
  73     @entry.quality_trim_right!(38)
  74     assert_equal("AAAAATC", @entry.seq)
  75     assert_equal("hhhhhgf", @entry.qual)
  76   end
  77
  78   def test_Trim_quality_trim_right_with_all_low_qual_returns_correctly
  79     @entry.seq  = "GCTAAAAA"
  80     @entry.qual = "@@@@@@@@"
  81     @entry.quality_trim_right!(38)
  82     assert_equal("", @entry.seq)
  83     assert_equal("", @entry.qual)
  84   end
  85
  86   def test_Trim_quality_trim_left_returns_correctly
  87     @entry.seq  = "GCTAAAAA"
  88     @entry.qual = "efghhhhh"
  89     new_entry = @entry.quality_trim_left(38)
  90     assert_equal("CTAAAAA", new_entry.seq)
  91     assert_equal("fghhhhh", new_entry.qual)
  92     assert_equal("GCTAAAAA", @entry.seq)
  93     assert_equal("efghhhhh", @entry.qual)
  94   end
  95
  96   def test_Trim_quality_trim_left_bang_returns_correctly
  97     @entry.seq  = "GCTAAAAA"
  98     @entry.qual = "efghhhhh"
  99     @entry.quality_trim_left!(38)
 100     assert_equal("CTAAAAA", @entry.seq)
 101     assert_equal("fghhhhh", @entry.qual)
 102   end
 103
 104   def test_Trim_quality_trim_left_with_all_low_qual_returns_correctly
 105     @entry.seq  = "GCTAAAAA"
 106     @entry.qual = "@@@@@@@@"
 107     @entry.quality_trim_left!(38)
 108     assert_equal("", @entry.seq)
 109     assert_equal("", @entry.qual)
 110   end
 111
 112   def test_Trim_quality_trim_returns_correctly
 113     @entry.seq  = "GCTAAAAAGTG"
 114     @entry.qual = "efghhhhhgfe"
 115     new_entry = @entry.quality_trim(38)
 116     assert_equal("CTAAAAAGT", new_entry.seq)
 117     assert_equal("fghhhhhgf", new_entry.qual)
 118     assert_equal("GCTAAAAAGTG", @entry.seq)
 119     assert_equal("efghhhhhgfe", @entry.qual)
 120   end
 121
 122   def test_Trim_quality_trim_bang_returns_correctly
 123     @entry.seq  = "GCTAAAAAGTG"
 124     @entry.qual = "efghhhhhgfe"
 125     @entry.quality_trim!(38)
 126     assert_equal("CTAAAAAGT", @entry.seq)
 127     assert_equal("fghhhhhgf", @entry.qual)
 128   end
 129
 130   def test_Trim_quality_trim_with_min_len_bang_returns_correctly
 131     @entry.seq  = "GCTCAAACGTG"
 132     @entry.qual = "hdefghgfedh"
 133     @entry.quality_trim!(37, 2)
 134     assert_equal("TCAAACG", @entry.seq)
 135     assert_equal("efghgfe", @entry.qual)
 136   end
 137
 138   def test_Trim_quality_trim_with_all_low_qual_returns_correctly
 139     @entry.seq  = "GCTCAAACGTG"
 140     @entry.qual = "@@@@@@@@@@@"
 141     @entry.quality_trim!(37, 2)
 142     assert_equal("", @entry.seq)
 143     assert_equal("", @entry.qual)
 144   end
 145 end
 146
 147 __END__