在文本中查找相似的行 - 階段 - 動態比較

Question

我有一個小生物信息學問題，我認爲應該很容易解決。與「基因型分期」有關。但我不知道如何解決它。 在下面的摘錄中，第一列是標識符，後續列是用「a」或「b」標記的二元基因型。 「 - 」表示缺少值。

Si_gnF.scaffold10533.53688bp_tag414456 b a a b b a b a a a b a b b a b a a b b a a b b 
Si_gnF.scaffold10533.76297bp_tag414484 a b b a a b a b b b a b a a b a b b a - b b a a 
Si_gnF.scaffold10533.98416bp_tag414526 a b b a a b a b b b a b a a b a b b a a b b a a 
Si_gnF.scaffold10534.48805bp_tag414546 b a a b a b a b b b b b b a a a a b a b b b b a 
Si_gnF.scaffold10535.1091787bp_tag414684 a a a b b a a a b a b a a a a b b b a a b b a a 
Si_gnF.scaffold10535.1151107bp_tag414765 b b b a a b b b a b a - b b b a a a b b a a b b 
Si_gnF.scaffold10535.1220879bp_tag414877 a a a b b a a a b a b a a a a b b b a a b b a a 
Si_gnF.scaffold10535.1304464bp_tag414988 b b b a a b b b a b a b b b b a a a b b a a b b 
Si_gnF.scaffold10535.1347462bp_tag415047 b b b a a b b b a b a b b b b a a a b b a a b b 
Si_gnF.scaffold10535.1379804bp_tag415090 b b b a a b b b a b a b b b b a a a b b a a b b 
Si_gnF.scaffold10535.1540335bp_tag415345 a a a b b a a a b a b a a a a b b b a a b b a a 
Si_gnF.scaffold10535.1585442bp_tag415410 a a a b b a a a b a b a a a a b b b a a b b a a 
Si_gnF.scaffold10535.1609908bp_tag415431 b b b a a b a b a b a b b b b a a a b b a a b b 
Si_gnF.scaffold10535.1711158bp_tag415567 b b b a a b b b a b a b b b b a a a b b a a b b 
Si_gnF.scaffold10535.1744394bp_tag415609 b b b a a b b b a b a b b b b a a a b b a a b b 
Si_gnF.scaffold10535.1751886bp_tag415620 a a a b b a a a b a b a a a a b b b a a b b a a 
Si_gnF.scaffold10535.1752774bp_tag415622 a a a b b a a a b a b a a a a b b b a a b b a a 
Si_gnF.scaffold10535.1789478bp_tag415675 b b - a a b b b a b a b b b b a a a b b a a b b 
Si_gnF.scaffold10535.1800135bp_tag415687 b b b a a b b b a b a b b b b a a a b b a a b b 
Si_gnF.scaffold10535.1885424bp_tag415814 a a a b b a a a b a b a a a a b b b a a b b a a 

基本上，我想盡量減少行之間的差異數量。 （我無法編輯單個列，但可以翻轉整行標籤）。前四條線的結果是這樣的：

Si_gnF.scaffold10533.53688bp_tag414456 b a a b b a b a a a b a b b a b a a b b a a b b 
Si_gnF.scaffold10533.76297bp_tag414484 b a a b b a b a a a b a b b a b a a b - a a b b <-- this one flipped 
Si_gnF.scaffold10533.98416bp_tag414526 b a a b b a b a a a b a b b a b a a b b a a b b <-- this one flipped 
Si_gnF.scaffold10533.53688bp_tag414456 b a a b b a b a a a b a b b a b a a b b a a b b 

作爲第一步，我需要進行配對比較。但是量化差異的好方法是什麼，以便我知道哪些行必須翻轉標籤？ （連續兩行很少匹配100％;可能有多個（甚至很多）不匹配以及缺失值）。

（最好在紅寶石或R）

Answer 1

可以使用Levenshtein算法來量化兩個字符串之間的區別。一種方式做到這一點：

require 'text' # See http://rubygems.org/gems/text 

lines # => a array with each line 

def compare(line1, line2) 
    Text::Levenshtein.distance(line1.sub(/.*\s/, '').sort, 
          line2.sub(/.*\s/, '').sort) 
end 

compare(lines[0], lines[1]) # => 1 (one value different) 

（如果「abaa中」不等於「AAAB」，從方法去除sort）