code_ruby/test/maasha/seq/test_assemble.rb

   1 #!/usr/bin/env ruby
   2 $:.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
   3
   4 require 'maasha/seq/assemble'
   5 require 'test/unit'
   6 require 'test/helper'
   7 require 'pp'
   8
   9 class TestAssemble < Test::Unit::TestCase
  10   test "Assemble.pair without overlap returns nil" do
  11     assert_nil(Assemble.pair(Seq.new(seq: "aaaa"), Seq.new(seq: "tttt")))
  12   end
  13
  14   test "Assemble.pair with overlap returns correctly" do
  15     assert_equal("atcGatc", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "gatc")).seq)
  16     assert_equal("atCGat",  Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "cgat")).seq)
  17     assert_equal("aTCGa",   Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "tcga")).seq)
  18     assert_equal("ATCG",    Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "atcg")).seq)
  19   end
  20
  21   test "Assemble.pair with first sequence longer than second and terminal overlap returns correctly" do
  22     e1 = Seq.new(seq_name: "t1", seq: "AGGCGT")
  23     e2 = Seq.new(seq_name: "t2", seq: "GT")
  24     a = Assemble.pair(e1, e2)
  25     assert_equal("t1:overlap=2:hamming=0", a.seq_name)
  26     assert_equal("aggcGT", a.seq)
  27   end
  28
  29   test "Assemble.pair with first sequence longer than second and internal overlap returns correctly" do
  30     e1 = Seq.new(seq_name: "t1", seq: "AGGCGT")
  31     e2 = Seq.new(seq_name: "t2", seq: "GC")
  32     a = Assemble.pair(e1, e2)
  33     assert_equal("t1:overlap=2:hamming=0", a.seq_name)
  34     assert_equal("agGCgt", a.seq)
  35   end
  36
  37   test "Assemble.pair with first sequence longer than second and initial overlap returns correctly" do
  38     e1 = Seq.new(seq_name: "t1", seq: "GTCAGA")
  39     e2 = Seq.new(seq_name: "t2", seq: "GT")
  40     a = Assemble.pair(e1, e2)
  41     assert_equal("t1:overlap=2:hamming=0", a.seq_name)
  42     assert_equal("GTcaga", a.seq)
  43   end
  44
  45   test "Assemble.pair with first sequence shorter than second and initial overlap returns correctly" do
  46     e1 = Seq.new(seq_name: "t1", seq: "AG")
  47     e2 = Seq.new(seq_name: "t2", seq: "AGTCAG")
  48     a = Assemble.pair(e1, e2)
  49     assert_equal("t1:overlap=2:hamming=0", a.seq_name)
  50     assert_equal("AGtcag", a.seq)
  51   end
  52
  53   test "Assemble.pair with overlap and overlap_min returns correctly" do
  54     assert_nil(Assemble.pair(Seq.new(seq: "atcg"), Seq.new(seq: "gatc"), :overlap_min => 2))
  55     assert_equal("atCGat", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "cgat"), :overlap_min => 2).seq)
  56   end
  57
  58   test "Assemble.pair with overlap and overlap_max returns correctly" do
  59     assert_equal("aTCGa", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "tcga"), :overlap_max => 3).seq)
  60     assert_nil(Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "atcg"), :overlap_max => 3))
  61   end
  62
  63   test "Assemble.pair with overlap returns correct quality" do
  64     assert_equal("?", Assemble.pair(Seq.new(seq_name: "t1", seq: "a", qual: "I"), Seq.new(seq_name: "t2", seq: "a", qual: "5")).qual)
  65     assert_equal("GH??43", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg", qual: "GHII"), Seq.new(seq_name: "t2", seq: "cgat", qual: "5543")).qual)
  66     assert_equal("I???5", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg", qual: "IIII"), Seq.new(seq_name: "t2", seq: "tcga", qual: "5555")).qual)
  67   end
  68
  69   test "Assemble.pair with mismatch returns the highest scoring" do
  70     assert_equal("ATCGA", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcga", qual: "IIIII"), Seq.new(seq_name: "t2", seq: "attga", qual: "55555"), :mismatches_max => 20).seq)
  71     assert_equal("ATTGA", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcga", qual: "55555"), Seq.new(seq_name: "t2", seq: "attga", qual: "IIIII"), :mismatches_max => 20).seq)
  72   end
  73 end