gene-matcher 0.1.5 → 0.1.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f451b24184e517be0bfdf398c1ad227be0c956a7e3173f7a31a45530af64291d
-  data.tar.gz: ee44f41ce12e8ac4a311c58a59339621230513bbe6202083bae3f044f830f4c6
+  metadata.gz: b8157bdd5dae107a5180e78d51de4a146b0768b4d8d8b8e638e61ec23ad8d6c6
+  data.tar.gz: 4dc38fa6ecccd8a31f77e96a672ee76d047f55af4957a28bf931c75a8483d45d
 SHA512:
-  metadata.gz: 7237131d90e3fed9a1f935c818bd75c8179a3de6a0bbcf4b7073cced5c3bc314a769680e73cfe46f3f228328427e447e0ee7fb22ec632920eea0b14c29510c98
-  data.tar.gz: 27614deb05f5649814174f3c5e4f8b771d3610c4dd9d8034409326f7dff77a32140e1fd038e6f055b1aa1661f0d3ea7ffe18cd0856617bd30c524ef5a28ee9b2
+  metadata.gz: 5333cfbcc037c18bb67cb140d49018af1e696260ff6268e4c1f5a968e4753fc138425bba5fd96f1928ef9cece8200a957a4f1607ec99ed792f64dff0ea0f77e4
+  data.tar.gz: fc5ff17d69865a118262ec29da7127bf2eae5e7aadad22697bc5c606e668acbccbd848b6caa470be9eafac04dd2dcc5e364a7cb876eab95f659d6d73d2931056

data/lib/alignment.rb

@@ -1,12 +1,10 @@
 class Alignment
-  attr_accessor :score, :alignmentI, :alignmentJ, :startI, :startJ, :endI, :endJ, :reversed, :aside, :source
+  attr_accessor :alignmentI, :alignmentJ, :startI, :startJ, :endI, :endJ, :reversed, :aside, :source
 
   BLANK = "-"
 
   def initialize(h=nil)
     return init_from_hash(h) if h
-    # スコア
-    @score = 0
     # 検索対象（データベースに入っていた）配列
     @alignmentI = ""
     # 検索した（クエリ=入力された）配列
@@ -27,7 +25,6 @@ class Alignment
 
   def init_from_hash(h)
     # 引数のハッシュから初期化
-    @score = h["score"]
     @alignmentI = h["alignmentI"]
     @alignmentJ = h["alignmentJ"]
     @startI = h["startI"]
@@ -42,7 +39,6 @@ class Alignment
   def to_h
     # ハッシュに変換
     h = {}
-    h["score"] = @score
     h["alignmentI"] = @alignmentI
     h["alignmentJ"] = @alignmentJ
     h["startI"] = @startI
@@ -87,7 +83,18 @@ class Alignment
   def number_of_blank
   end
 
+  def score_a
+    return 0 if @alignmentI.length == 0
+    return alignment_count / @alignmentI.length.to_f
+  end
+
+  def score(thresh=20)
+    # 長さがthresh以下なら0を返す
+    return 0 if @alignmentI.length < thresh
+    return alignment_count * score_a
+  end
+
   def to_s
-    "score=#{@score} I=" + @alignmentI + " J=" + @alignmentJ;
+    "score=#{score} I=" + @alignmentI + " J=" + @alignmentJ;
   end
 end

data/lib/gene-matcher.rb

@@ -14,8 +14,9 @@ class Matcher
   def scan(target_sequence,source = {})
     sw = SmithWaterman.instance
     a = sw.alignment(target_sequence, @input_sequence)
-    a.source = source
-    @alignments += [a] if a.score >= @limit
+    a.source = {target_sequence: target_sequence}.merge(source)
+    puts "#{a.score} / #{a.alignment_count} = #{a.score / a.alignment_count}" if ENV["DEBUG"]
+    @alignments += [a] if a.score / a.alignment_count >= @limit
   end
 end
 

data/lib/smith-waterman.rb

@@ -88,11 +88,7 @@ class SmithWaterman
     a.startI = i
     a.startJ = j
 
-    if a.alignmentI.length <= 20
-      a.score = 0
-    else
-      a.score = a.alignment_count ** 2 / a.alignmentI.length.to_f
-    end
+    # スコアはここでは求めない(Java版ではここで決定していた)
     return a
   end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: gene-matcher
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 0.1.7
 platform: ruby
 authors:
 - ITO Yosei
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-08-31 00:00:00.000000000 Z
+date: 2023-09-11 00:00:00.000000000 Z
 dependencies: []
 description: Algorithm for determining similar regions between nucleic acid sequences.
 email: y-itou@lumber-mill.co.jp