added patscan_trim method to Seq

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

diff --git a/code_ruby/lib/maasha/seq/trim.rb b/code_ruby/lib/maasha/seq/trim.rb
index e7e9bb1daf6b019e77e78b8eabf44cad1abc2ea5..2be3e56800a518a25ce5da5665053b0951d4de8e 100644 (file)
--- a/code_ruby/lib/maasha/seq/trim.rb
+++ b/code_ruby/lib/maasha/seq/trim.rb
@@ -23,6 +23,9 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'inline'
+require 'maasha/seq/backtrack'
+
+include BackTrack
 
 # Error class for all exceptions to do with Trim.
 class TrimError < StandardError; end
@@ -96,6 +99,38 @@ module Trim
     self.subseq!(pos_left, pos_right - pos_left)
   end
 
+  # Method to locate a pattern in a sequence and trim all sequence to the left
+  # including the pattern.
+  def patmatch_trim_left!(pattern, options = {})
+    match = self.patmatch(pattern, options)
+
+    if match
+      stop = self.length
+
+      self.seq  = self.seq[match.pos + match.length .. stop]
+      self.qual = self.qual[match.pos + match.length .. stop] if self.qual
+
+      return self
+    end
+
+    nil
+  end
+
+  # Method to locate a pattern in a sequence and trim all sequence to the right
+  # including the pattern.
+  def patmatch_trim_right!(pattern, options = {})
+    match = self.patmatch(pattern, options)
+
+    if match
+      self.seq  = self.seq[0 ... match.pos]
+      self.qual = self.qual[0 ... match.pos] if self.qual
+
+      return self
+    end
+
+    nil
+  end
+
   private
 
   # Method to check the arguments for trimming and raise on bad sequence, qualities,