added amiguity.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2200 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/seq/ambiguity.rb b/code_ruby/lib/maasha/seq/ambiguity.rb
new file mode 100644 (file)
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+++ b/code_ruby/lib/maasha/seq/ambiguity.rb
@@ -0,0 +1,71 @@
+# Copyright (C) 2013 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'inline'
+#autoload :NArray, 'narray'
+
+module Ambiguity
+  # IUPAC alphabet and binary encoding of the same
+  # http://en.wikipedia.org/wiki/Nucleic_acid_notation
+
+  AMBIGUITY_STR = "ACGTUWSMKRYBDHVNacgtuwsmkrybdhvn"
+  AMBIGUITY_BIN = "\x08\x04\x02\x01\x01\x09\x06\x0c\x03\x0a\x05\x07\x0b\x0d\x0e\x0f\x08\x04\x02\x01\x01\x09\x06\x0c\x03\x0a\x05\x07\x0b\x0d\x0e\x0f"
+
+  def self.hamming_distance(seq1, seq2)
+    (NArray.to_na(seq1.tr(AMBIGUITY_STR, AMBIGUITY_BIN), 'byte') &
+     NArray.to_na(seq2.tr(AMBIGUITY_STR, AMBIGUITY_BIN), 'byte')).eq(0).sum
+  end
+
+  def add_ambiguity_macro inline_builder
+    # Macro for matching nucleotides including ambiguity codes.
+    inline_builder.prefix %{
+      #define MATCH(A,B) ((bitmap[A] & bitmap[B]) != 0)
+    }
+
+    # Bitmap for matching nucleotides including ambiguity codes.
+    # For each value bits are set from the left: bit pos 1 for A,
+    # bit pos 2 for T, bit pos 3 for C, and bit pos 4 for G.
+    inline_builder.prefix %{
+      char bitmap[256] = {
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0,
+          0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0,
+          0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0,
+          0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
+      };
+    }
+  end
+end
+