class TestAssemble < Test::Unit::TestCase
test "Assemble.pair without overlap returns nil" do
- assert_nil(Assemble.pair(Seq.new("test1", "aaaa"), Seq.new("test2", "tttt")))
+ assert_nil(Assemble.pair(Seq.new(seq: "aaaa"), Seq.new(seq: "tttt")))
end
- test "Assemble.pair with overlap returns the correctly" do
- assert_equal("atcGatc", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc")).seq)
- assert_equal("atCGat", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat")).seq)
- assert_equal("aTCGa", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga")).seq)
- assert_equal("ATCG", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg")).seq)
+ test "Assemble.pair with overlap returns correctly" do
+ assert_equal("atcGatc", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "gatc")).seq)
+ assert_equal("atCGat", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "cgat")).seq)
+ assert_equal("aTCGa", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "tcga")).seq)
+ assert_equal("ATCG", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "atcg")).seq)
end
test "Assemble.pair with overlap and overlap_min returns correctly" do
- assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc"), :overlap_min => 2))
- assert_equal("atCGat", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat"), :overlap_min => 2).seq)
+ assert_nil(Assemble.pair(Seq.new(seq: "atcg"), Seq.new(seq: "gatc"), :overlap_min => 2))
+ assert_equal("atCGat", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "cgat"), :overlap_min => 2).seq)
end
test "Assemble.pair with overlap and overlap_max returns correctly" do
- assert_equal("aTCGa", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga"), :overlap_max => 3).seq)
- assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg"), :overlap_max => 3))
+ assert_equal("aTCGa", Assemble.pair(Seq.new(seq_name: "t1", seq: "atcg"), Seq.new(seq_name: "t2", seq: "tcga"), :overlap_max => 3).seq)
+ assert_nil(Assemble.pair(Seq.new(seq: "atcg"), Seq.new(seq: "atcg"), :overlap_max => 3))
end
test "Assemble.pair with overlap returns correct quality" do
- assert_equal("?", Assemble.pair(Seq.new("test1", "a", :dna, "I"), Seq.new("test2", "a", :dna, "5")).qual)
- assert_equal("GH??43", Assemble.pair(Seq.new("test1", "atcg", :dna, "GHII"), Seq.new("test2", "cgat", :dna, "5543")).qual)
- assert_equal("I???5", Assemble.pair(Seq.new("test1", "atcg", :dna, "IIII"), Seq.new("test2", "tcga", :dna, "5555")).qual)
+ assert_equal("?", Assemble.pair(Seq.new(seq_name: "t1", seq: "a", qual: "I"), Seq.new(seq_name: "t2", seq: "a", qual: "5")).qual)
+ 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)
+ 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)
end
test "Assemble.pair with mismatch returns the highest scoring" do
- assert_equal("ATCGA", Assemble.pair(Seq.new("t1", "atcga", :dna, "IIIII"), Seq.new("t2", "attga", :dna, "55555"), :mismatches_max => 20).seq)
- assert_equal("ATTGA", Assemble.pair(Seq.new("t1", "atcga", :dna, "55555"), Seq.new("t2", "attga", :dna, "IIIII"), :mismatches_max => 20).seq)
+ 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)
+ 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)
end
end