refactoring of revcomp in seq.rb

[biopieces.git] / code_ruby / lib / maasha / seq.rb

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index e72250d596cc5d1dd55adac34d3a15b3503048fa..4a0af47ed0f5fde9d5ffe87ca19a3caec087f6d6 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -150,6 +150,7 @@ class Seq
   # by inspecting the first 100 residues.
   def type_guess!
     self.type = self.type_guess
+    self
   end
 
   # Returns the length of a sequence.
@@ -334,17 +335,13 @@ class Seq
     key
   end
 
-  # Method to reverse complement sequence.
-  def reverse_complement
-    self.reverse
-    self.complement
-    self
+  # Method to reverse the sequence.
+  def reverse
+    Seq.new(self.seq_name, self.seq.reverse, self.type, self.qual ? self.qual.reverse : self.qual)
   end
 
-  alias :revcomp :reverse_complement
-
   # Method to reverse the sequence.
-  def reverse
+  def reverse!
     self.seq.reverse!
     self.qual.reverse! if self.qual
     self
@@ -354,6 +351,26 @@ class Seq
   def complement
     raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
 
+    entry          = Seq.new
+    entry.seq_name = self.seq_name
+    entry.type     = self.type
+    entry.qual     = self.qual
+
+    if self.is_dna?
+      entry.seq = self.seq.tr('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
+    elsif self.is_rna?
+      entry.seq = self.seq.tr('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn')
+    else
+      raise SeqError, "Cannot complement sequence type: #{self.type}"
+    end
+
+    entry
+  end
+
+  # Method that complements sequence including ambiguity codes.
+  def complement!
+    raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
+
     if self.is_dna?
       self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
     elsif self.is_rna?
@@ -361,6 +378,8 @@ class Seq
     else
       raise SeqError, "Cannot complement sequence type: #{self.type}"
     end
+
+    self
   end
 
   # Method to determine the Hamming Distance between
@@ -488,21 +507,6 @@ class Seq
     ((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
   end
 
-  # Hard masks sequence residues where the corresponding quality score
-  # is below a given cutoff.
-  def mask_seq_hard_old(cutoff)
-    seq    = self.seq.upcase
-    scores = self.qual
-    i      = 0
-
-    scores.each_char do |score|
-      seq[i] = 'N' if score.ord - SCORE_BASE < cutoff
-      i += 1 
-    end
-
-    self.seq = seq
-  end
-
   # Hard masks sequence residues where the corresponding quality score
   # is below a given cutoff.
   def mask_seq_hard!(cutoff)