2 $:.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
4 require 'maasha/seq/assemble'
9 class TestAssemble < Test::Unit::TestCase
10 test "Assemble.pair without overlap returns nil" do
11 assert_nil(Assemble.pair(Seq.new("test1", "aaaa"), Seq.new("test2", "tttt")))
14 test "Assemble.pair with overlap returns the correctly" do
15 assert_equal("ATCgATC", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc")).seq)
16 assert_equal("ATcgAT", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat")).seq)
17 assert_equal("AtcgA", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga")).seq)
18 assert_equal("atcg", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg")).seq)
21 test "Assemble.pair with overlap and overlap_min returns correctly" do
22 assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc"), :overlap_min => 2))
23 assert_equal("ATcgAT", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat"), :overlap_min => 2).seq)
26 test "Assemble.pair with overlap and overlap_max returns correctly" do
27 assert_equal("AtcgA", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga"), :overlap_max => 3).seq)
28 assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg"), :overlap_max => 3))
31 test "Assemble.pair with overlap returns correct quality" do
32 assert_equal("?", Assemble.pair(Seq.new("test1", "a", :dna, "I"), Seq.new("test2", "a", :dna, "5")).qual)
33 assert_equal("GH??43", Assemble.pair(Seq.new("test1", "atcg", :dna, "GHII"), Seq.new("test2", "cgat", :dna, "5543")).qual)
34 assert_equal("I???5", Assemble.pair(Seq.new("test1", "atcg", :dna, "IIII"), Seq.new("test2", "tcga", :dna, "5555")).qual)
37 test "Assemble.pair with mismatch returns the highest scoring" do
38 assert_equal("atcga", Assemble.pair(Seq.new("t1", "atcga", :dna, "IIIII"), Seq.new("t2", "attga", :dna, "55555"), :mismatches_max => 20).seq)
39 assert_equal("attga", Assemble.pair(Seq.new("t1", "atcga", :dna, "55555"), Seq.new("t2", "attga", :dna, "IIIII"), :mismatches_max => 20).seq)