From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 13 Mar 2013 09:12:52 +0000 (+0000)
Subject: upgraded assemble.rb to chose proper residue when mismatch
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=8baaff296bcb2be5030906d02a36e5a27cb9d064

upgraded assemble.rb to chose proper residue when mismatch

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2137 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/seq/assemble.rb b/code_ruby/lib/maasha/seq/assemble.rb
index e59e178..7745b5b 100644
--- a/code_ruby/lib/maasha/seq/assemble.rb
+++ b/code_ruby/lib/maasha/seq/assemble.rb
@@ -48,22 +48,22 @@ class Assemble
       hamming_dist = (na_seq1[-1 * overlap .. -1] ^ na_seq2[0 ... overlap]).count_true
 
       if hamming_dist <= percent2real(overlap, @options[:mismatches_max])
-        merged = @entry1 + @entry2[overlap .. -1]
+        entry_left  = @entry1[0 ... @entry1.length - overlap]
+        entry_right = @entry2[overlap .. -1]
 
         if @entry1.qual and @entry2.qual
-          qual1 = @entry1.qual[@entry1.length - overlap .. -1]
-          qual2 = @entry2.qual[0 ... overlap]
+          entry_overlap1 = @entry1[-1 * overlap .. -1]
+          entry_overlap2 = @entry2[0 ... overlap]
 
-          na_qual1 = NArray.to_na(qual1, "byte")
-          na_qual2 = NArray.to_na(qual2, "byte")
-
-          qual = ((na_qual1 + na_qual2) / 2).to_s
-
-          merged.seq_name = @entry1.seq_name + ":overlap=#{overlap}:hamming=#{hamming_dist}"
-          merged.qual[@entry1.length - overlap ... @entry1.length]  = qual
+          entry_overlap = merge_overlap(entry_overlap1, entry_overlap2)
+        else
+          entry_overlap = @entry1[-1 * overlap .. -1]
         end
 
-        return merged
+        entry_merged          = entry_left + entry_overlap + entry_right
+        entry_merged.seq_name = @entry1.seq_name + ":overlap=#{overlap}:hamming=#{hamming_dist}"
+
+        return entry_merged
       end
 
       overlap -= 1
@@ -71,7 +71,26 @@ class Assemble
   end
 
   def percent2real(length, percent)
-      (length * percent * 0.01).round
+    (length * percent * 0.01).round
+  end
+
+  def merge_overlap(entry_overlap1, entry_overlap2)
+    na_seq = NArray.byte(entry_overlap1.length, 2)
+    na_seq[true, 0] = NArray.to_na(entry_overlap1.seq.downcase, "byte")
+    na_seq[true, 1] = NArray.to_na(entry_overlap2.seq.downcase, "byte")
+
+    na_qual = NArray.byte(entry_overlap1.length, 2)
+    na_qual[true, 0] = NArray.to_na(entry_overlap1.qual, "byte")
+    na_qual[true, 1] = NArray.to_na(entry_overlap2.qual, "byte")
+
+    mask_xor = na_seq[true, 0] ^ na_seq[true, 1] > 0
+    mask_seq = ((na_qual * mask_xor).eq( (na_qual * mask_xor).max(1)))
+
+    merged      = Seq.new()
+    merged.seq  = (na_seq * mask_seq).max(1).to_s
+    merged.qual = na_qual.mean(1).round.to_type("byte").to_s
+
+    merged
   end
 end
 
diff --git a/code_ruby/test/maasha/seq/test_assemble.rb b/code_ruby/test/maasha/seq/test_assemble.rb
index bdc759c..cf05ca8 100755
--- a/code_ruby/test/maasha/seq/test_assemble.rb
+++ b/code_ruby/test/maasha/seq/test_assemble.rb
@@ -33,4 +33,9 @@ class TestAssemble < Test::Unit::TestCase
     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)
   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)
+  end
 end