X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=blobdiff_plain;f=code_ruby%2Ftest%2Fmaasha%2Fseq%2Ftest_assemble.rb;h=bd1baf0649390f0a2cbabc382af0d9cce9b551a8;hp=b5ddb7d706c03b3b4ea633149b8e55f7741785e6;hb=a30677c14f1738f6a76e8c12f2e732cdef9958d6;hpb=545eed9d7927e2c59a7c7d3c919aa8d8bed18c86

diff --git a/code_ruby/test/maasha/seq/test_assemble.rb b/code_ruby/test/maasha/seq/test_assemble.rb
index b5ddb7d..bd1baf0 100755
--- a/code_ruby/test/maasha/seq/test_assemble.rb
+++ b/code_ruby/test/maasha/seq/test_assemble.rb
@@ -8,34 +8,34 @@ require 'pp'
 
 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