From b2ea0b5a51a558478af60e9df4c643dd58552086 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 21 Jun 2013 09:35:03 +0000
Subject: [PATCH] added edit_distance method to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2184 74ccb610-7750-0410-82ae-013aeee3265d
---
code_ruby/lib/maasha/seq.rb | 18 ++++++++++------
.../test/maasha/{ => seq}/test_levenshtein.rb | 21 ++++++++++++-------
code_ruby/test/maasha/test_seq.rb | 9 ++++++--
3 files changed, 33 insertions(+), 15 deletions(-)
rename code_ruby/test/maasha/{ => seq}/test_levenshtein.rb (72%)
diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 2788e5d..e4b6bfd 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -27,9 +27,10 @@ require 'maasha/seq/digest'
require 'maasha/seq/trim'
require 'narray'
-autoload :BackTrack, 'maasha/seq/backtrack.rb'
-autoload :Dynamic, 'maasha/seq/dynamic.rb'
-autoload :Homopolymer, 'maasha/seq/homopolymer.rb'
+autoload :BackTrack, 'maasha/seq/backtrack'
+autoload :Dynamic, 'maasha/seq/dynamic'
+autoload :Homopolymer, 'maasha/seq/homopolymer'
+autoload :Levenshtein, 'maasha/seq/levenshtein'
# Residue alphabets
DNA = %w[a t c g]
@@ -68,7 +69,6 @@ TRANS_TAB11 = {
"GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
}
-
# Error class for all exceptions to do with Seq.
class SeqError < StandardError; end
@@ -384,8 +384,14 @@ class Seq
# Method to determine the Hamming Distance between
# two Sequence objects (case insensitive).
- def hamming_distance(seq)
- self.seq.upcase.hamming_distance(seq.seq.upcase)
+ def hamming_distance(entry)
+ self.seq.upcase.hamming_distance(entry.seq.upcase)
+ end
+
+ # Method to determine the Edit Distance between
+ # two Sequence objects (case insensitive).
+ def edit_distance(entry)
+ Levenshtein.distance(self.seq, entry.seq)
end
# Method that generates a random sequence of a given length and type.
diff --git a/code_ruby/test/maasha/test_levenshtein.rb b/code_ruby/test/maasha/seq/test_levenshtein.rb
similarity index 72%
rename from code_ruby/test/maasha/test_levenshtein.rb
rename to code_ruby/test/maasha/seq/test_levenshtein.rb
index fca9029..a260829 100755
--- a/code_ruby/test/maasha/test_levenshtein.rb
+++ b/code_ruby/test/maasha/seq/test_levenshtein.rb
@@ -27,27 +27,34 @@ $:.unshift File.join(File.dirname(__FILE__), '..', '..')
require 'test/unit'
require 'test/helper'
-require 'maasha/levenshtein'
+require 'maasha/seq/levenshtein'
class LevenshteinTest < Test::Unit::TestCase
test "Levenshtein.distance returns 0 with identical strings" do
- assert_equal(0, Levenshtein.distance("foo", "foo"))
+ assert_equal(0, Levenshtein.distance("atcg", "atcg"))
end
test "Levenshtein.distance returns s length if t is empty" do
- assert_equal(3, Levenshtein.distance("foo", ""))
+ assert_equal(4, Levenshtein.distance("atcg", ""))
end
test "Levenshtein.distance returns t length if s is empty" do
- assert_equal(5, Levenshtein.distance("", "fobar"))
+ assert_equal(5, Levenshtein.distance("", "atcgn"))
end
test "Levenshtein.distance with mismatch only returns correctly" do
- assert_equal(1, Levenshtein.distance("foo", "fox"))
+ assert_equal(1, Levenshtein.distance("atcg", "atgg"))
+ end
+
+ test "Levenshtein.distance with ambiguity code returns correctly" do
+ assert_equal(0, Levenshtein.distance("atcg", "nnnn"))
+ end
+
+ test "Levenshtein.distance with insertion returns correctly" do
+ assert_equal(1, Levenshtein.distance("atcg", "attcg"))
end
test "Levenshtein.distance returns correctly" do
- assert_equal(3, Levenshtein.distance("kitten", "sitting"))
- assert_equal(3, Levenshtein.distance("Saturday", "Sunday"))
+ assert_equal(2, Levenshtein.distance("atcg", "tgncg"))
end
end
diff --git a/code_ruby/test/maasha/test_seq.rb b/code_ruby/test/maasha/test_seq.rb
index 8eed8d5..5947ee8 100755
--- a/code_ruby/test/maasha/test_seq.rb
+++ b/code_ruby/test/maasha/test_seq.rb
@@ -298,13 +298,18 @@ class TestSeq < Test::Unit::TestCase
assert_equal("UAGCuagc", @entry.complement!.seq)
end
-
- test "#hamming distance returns correctly" do
+ test "#hamming_distance returns correctly" do
seq1 = Seq.new("test1", "ATCG")
seq2 = Seq.new("test2", "atgg")
assert_equal(1, seq1.hamming_distance(seq2))
end
+ test "#edit_distance returns correctly" do
+ seq1 = Seq.new("test1", "ATCG")
+ seq2 = Seq.new("test2", "tgncg")
+ assert_equal(2, seq1.edit_distance(seq2))
+ end
+
test "#generate with length < 1 raises" do
assert_raise(SeqError) { @entry.generate(-10, :dna) }
assert_raise(SeqError) { @entry.generate(0, :dna) }
--
2.39.5