From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 13 Mar 2013 11:51:30 +0000 (+0000)
Subject: fixed minor upcase bug in assemble.rb
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=bc7b9f68c35624bd8a605e35f9a15dfbf66ae37d

fixed minor upcase bug in assemble.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2149 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/seq/assemble.rb b/code_ruby/lib/maasha/seq/assemble.rb
index dffbf11..7b02d03 100644
--- a/code_ruby/lib/maasha/seq/assemble.rb
+++ b/code_ruby/lib/maasha/seq/assemble.rb
@@ -64,6 +64,8 @@ class Assemble
           entry_overlap = @entry1[-1 * overlap .. -1]
         end
 
+        entry_left.seq.upcase!
+        entry_right.seq.upcase!
         entry_merged          = entry_left + entry_overlap + entry_right
         entry_merged.seq_name = @entry1.seq_name + ":overlap=#{overlap}:hamming=#{hamming_dist}"
 
diff --git a/code_ruby/test/maasha/seq/test_assemble.rb b/code_ruby/test/maasha/seq/test_assemble.rb
index cf05ca8..e4901b4 100755
--- a/code_ruby/test/maasha/seq/test_assemble.rb
+++ b/code_ruby/test/maasha/seq/test_assemble.rb
@@ -12,19 +12,19 @@ class TestAssemble < Test::Unit::TestCase
   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("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)
   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_equal("ATcgAT", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "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_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))
   end