code_ruby/test/maasha/seq/test_trim.rb

   1 #!/usr/bin/env ruby
   2 $:.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
   3
   4 require 'maasha/seq'
   5 require 'test/unit'
   6 require 'test/helper'
   7 require 'pp'
   8
   9 class TestTrim < Test::Unit::TestCase
  10   def setup
  11     @entry = Seq.new
  12   end
  13
  14   test "Seq.quality_trim with missing seq raises" do
  15     @entry.qual = "hhhh"
  16     assert_raise(TrimError) { @entry.quality_trim_right(20) }
  17     assert_raise(TrimError) { @entry.quality_trim_right!(20) }
  18     assert_raise(TrimError) { @entry.quality_trim_left(20) }
  19     assert_raise(TrimError) { @entry.quality_trim_left!(20) }
  20     assert_raise(TrimError) { @entry.quality_trim(20) }
  21     assert_raise(TrimError) { @entry.quality_trim!(20) }
  22   end
  23
  24   test "Seq.quality_trim with missing qual raises" do
  25     @entry.seq = "ATCG"
  26     assert_raise(TrimError) { @entry.quality_trim_right(20) }
  27     assert_raise(TrimError) { @entry.quality_trim_right!(20) }
  28     assert_raise(TrimError) { @entry.quality_trim_left(20) }
  29     assert_raise(TrimError) { @entry.quality_trim_left!(20) }
  30     assert_raise(TrimError) { @entry.quality_trim(20) }
  31     assert_raise(TrimError) { @entry.quality_trim!(20) }
  32   end
  33
  34   test "Seq.quality_trim with bad min raises" do
  35     @entry.seq  = "ATCG"
  36     @entry.qual = "hhhh"
  37
  38     [-1, 41].each do |min|
  39       assert_raise(TrimError) { @entry.quality_trim_right(min) }
  40       assert_raise(TrimError) { @entry.quality_trim_right!(min) }
  41       assert_raise(TrimError) { @entry.quality_trim_left(min) }
  42       assert_raise(TrimError) { @entry.quality_trim_left!(min) }
  43       assert_raise(TrimError) { @entry.quality_trim(min) }
  44       assert_raise(TrimError) { @entry.quality_trim!(min) }
  45     end
  46   end
  47
  48   test "Seq.quality_trim with ok min dont raise" do
  49     @entry.seq  = "ATCG"
  50     @entry.qual = "hhhh"
  51
  52     [0, 40].each do |min|
  53       assert_nothing_raised { @entry.quality_trim_right(min) }
  54       assert_nothing_raised { @entry.quality_trim_right!(min) }
  55       assert_nothing_raised { @entry.quality_trim_left(min) }
  56       assert_nothing_raised { @entry.quality_trim_left!(min) }
  57       assert_nothing_raised { @entry.quality_trim(min) }
  58       assert_nothing_raised { @entry.quality_trim!(min) }
  59     end
  60   end
  61
  62   test "Seq.quality_trim_right returns correctly" do
  63     @entry.seq  = "AAAAATCG"
  64     @entry.qual = "IIIIIHGF"
  65     new_entry = @entry.quality_trim_right(38)
  66     assert_equal("AAAAATC", new_entry.seq)
  67     assert_equal("IIIIIHG", new_entry.qual)
  68     assert_equal("AAAAATCG", @entry.seq)
  69     assert_equal("IIIIIHGF", @entry.qual)
  70   end
  71
  72   test "Seq.quality_trim_right! returns correctly" do
  73     @entry.seq  = "AAAAATCG"
  74     @entry.qual = "IIIIIHGF"
  75     @entry.quality_trim_right!(38)
  76     assert_equal("AAAAATC", @entry.seq)
  77     assert_equal("IIIIIHG", @entry.qual)
  78   end
  79
  80   test "Seq.quality_trim_right! with all low qual returns correctly" do
  81     @entry.seq  = "GCTAAAAA"
  82     @entry.qual = "@@@@@@@@"
  83     @entry.quality_trim_right!(38)
  84     assert_equal("", @entry.seq)
  85     assert_equal("", @entry.qual)
  86   end
  87
  88   test "Seq.quality_trim_left returns correctly" do
  89     @entry.seq  = "GCTAAAAA"
  90     @entry.qual = "FGHIIIII"
  91     new_entry = @entry.quality_trim_left(38)
  92     assert_equal("CTAAAAA", new_entry.seq)
  93     assert_equal("GHIIIII", new_entry.qual)
  94     assert_equal("GCTAAAAA", @entry.seq)
  95     assert_equal("FGHIIIII", @entry.qual)
  96   end
  97
  98   test "Seq.quality_trim_left! returns correctly" do
  99     @entry.seq  = "GCTAAAAA"
 100     @entry.qual = "FGHIIIII"
 101     @entry.quality_trim_left!(38)
 102     assert_equal("CTAAAAA", @entry.seq)
 103     assert_equal("GHIIIII", @entry.qual)
 104   end
 105
 106   test "Seq.quality_trim_left! with all low qual returns correctly" do
 107     @entry.seq  = "GCTAAAAA"
 108     @entry.qual = "@@@@@@@@"
 109     @entry.quality_trim_left!(38)
 110     assert_equal("", @entry.seq)
 111     assert_equal("", @entry.qual)
 112   end
 113
 114   test "Seq.quality_trim returns correctly" do
 115     @entry.seq  = "GCTAAAAAGTG"
 116     @entry.qual = "FGHIIIIIHGF"
 117     new_entry = @entry.quality_trim(38)
 118     assert_equal("CTAAAAAGT", new_entry.seq)
 119     assert_equal("GHIIIIIHG", new_entry.qual)
 120     assert_equal("GCTAAAAAGTG", @entry.seq)
 121     assert_equal("FGHIIIIIHGF", @entry.qual)
 122   end
 123
 124   test "Seq.quality_trim! returns correctly" do
 125     @entry.seq  = "GCTAAAAAGTG"
 126     @entry.qual = "FGHIIIIIHGF"
 127     @entry.quality_trim!(38)
 128     assert_equal("CTAAAAAGT", @entry.seq)
 129     assert_equal("GHIIIIIHG", @entry.qual)
 130   end
 131
 132   test "Seq.quality_trim! with min len bang returns correctly" do
 133     @entry.seq  = "GCTCAAACGTG"
 134     @entry.qual = "IEFGHIHGFEI"
 135     @entry.quality_trim!(37, 2)
 136     assert_equal("TCAAACG", @entry.seq)
 137     assert_equal("FGHIHGF", @entry.qual)
 138   end
 139
 140   test "Seq.quality_trim! with all low qual returns correctly" do
 141     @entry.seq  = "GCTCAAACGTG"
 142     @entry.qual = "@@@@@@@@@@@"
 143     @entry.quality_trim!(37, 2)
 144     assert_equal("", @entry.seq)
 145     assert_equal("", @entry.qual)
 146   end
 147
 148   test "#patmatch_trim_right! without match don't trim" do
 149     @entry.seq  = "GCTCAAACGTG"
 150     @entry.patmatch_trim_left!("GAAAC")
 151     assert_equal("GCTCAAACGTG", @entry.seq)
 152   end
 153
 154   test "#patmatch_trim_right! without match returns nil" do
 155     @entry.seq  = "GCTCAAACGTG"
 156     assert_nil(@entry.patmatch_trim_left!("GAAAC"))
 157   end
 158
 159   test "#patmatch_trim_right! without qual trims correctly" do
 160     @entry.seq  = "GCTCAAACGTG"
 161     @entry.patmatch_trim_left!("AAAC")
 162     assert_equal("GTG", @entry.seq)
 163   end
 164
 165   test "#patmatch_trim_right! with qual trims correctly" do
 166     @entry.seq  = "GCTCAAACGTG"
 167     @entry.qual = "IEFGHIHGFEI"
 168     @entry.patmatch_trim_left!("AAAC")
 169     assert_equal("GTG", @entry.seq)
 170     assert_equal("FEI", @entry.qual)
 171   end
 172
 173   test "#patmatch_trim_left! without match trims correctly" do
 174     @entry.seq  = "GCTCAAACGTG"
 175     @entry.patmatch_trim_right!("GAAAC")
 176     assert_equal("GCTCAAACGTG", @entry.seq)
 177   end
 178
 179   test "#patmatch_trim_left! without match returns nil" do
 180     @entry.seq  = "GCTCAAACGTG"
 181     assert_nil(@entry.patmatch_trim_right!("GAAAC"))
 182   end
 183
 184   test "#patmatch_trim_left! without qual trims correctly" do
 185     @entry.seq  = "GCTCAAACGTG"
 186     @entry.patmatch_trim_right!("AAAC")
 187     assert_equal("GCTC", @entry.seq)
 188   end
 189
 190   test "#patmatch_trim_left! with qual trims correctly" do
 191     @entry.seq  = "GCTCAAACGTG"
 192     @entry.qual = "IEFGHIHGFEI"
 193     @entry.patmatch_trim_right!("AAAC")
 194     assert_equal("GCTC", @entry.seq)
 195     assert_equal("IEFG", @entry.qual)
 196   end
 197 end
 198
 199 __END__