revamped find_homopolymers

[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 f76466f583af2a18699f3aa4ee40f67fb88e250e..2788e5dcc02d78cdb9e3fd38ef83749bad158b79 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -27,8 +27,9 @@ require 'maasha/seq/digest'
 require 'maasha/seq/trim'
 require 'narray'
 
-autoload :BackTrack, 'maasha/seq/backtrack.rb'
-autoload :Dynamic,   'maasha/seq/dynamic.rb'
+autoload :BackTrack,   'maasha/seq/backtrack.rb'
+autoload :Dynamic,     'maasha/seq/dynamic.rb'
+autoload :Homopolymer, 'maasha/seq/homopolymer.rb'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -416,6 +417,15 @@ class Seq
     self
   end
 
+  # Method to add two Seq objects.
+  def +(entry)
+    new_entry = Seq.new()
+    new_entry.seq  = self.seq  + entry.seq
+    new_entry.type = self.type              if self.type == entry.type
+    new_entry.qual = self.qual + entry.qual if self.qual and entry.qual
+    new_entry
+  end
+
   # Method to concatenate sequence entries.
   def <<(entry)
     raise SeqError, "sequences of different types" unless self.type == entry.type
@@ -427,6 +437,25 @@ class Seq
     self
   end
 
+  # Index method for Seq objects.
+  def [](*args)
+    entry = Seq.new
+    entry.seq_name = self.seq_name
+    entry.seq      = self.seq[*args]
+    entry.type     = self.type
+    entry.qual     = self.qual[*args] unless self.qual.nil?
+
+    entry
+  end
+
+  # Index assignment method for Seq objects.
+  def []=(*args, entry)
+    self.seq[*args]  = entry.seq[*args]
+    self.qual[*args] = entry.qual[*args] unless self.qual.nil?
+
+    self
+  end
+
   # Method that returns a subsequence of from a given start position
   # and of a given length.
   def subseq(start, length = self.length - start)
@@ -487,23 +516,6 @@ class Seq
     comp
   end
 
-  # Method that returns the length of the longest homopolymeric stretch
-  # found in a sequence.
-  def homopol_max(min = 1)
-    return 0 if self.seq.nil? or self.seq.empty?
-
-    found = false
-
-    self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
-      found = true
-      min   = match.size > min ? match.size : min
-    end
-
-    return 0 unless found
- 
-    min
-  end
-
   # Method that returns the percentage of hard masked residues
   # or N's in a sequence.
   def hard_mask