added to_fastq method 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 a3fe78905159ab4edeee58fcd0067ee4aca2988c..a724339694f27558504f427c31fedcd95167d744 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -24,6 +24,7 @@
 
 require 'maasha/digest'
 require 'maasha/patternmatcher'
+require 'maasha/bits'
 #require 'maasha/patscan'
 
 # Residue alphabets
@@ -172,13 +173,26 @@ class Seq
 
     unless wrap.nil?
       seq.gsub!(/(.{#{wrap}})/) do |match|
-        match << "\n"
+        match << $/
       end
 
       seq.chomp!
     end
 
-    ">#{seq_name}\n#{seq}\n"
+    ">" + seq_name + $/ + seq + $/
+  end
+
+  # Method that given a Seq entry returns a FASTQ entry (a string).
+  def to_fastq
+    raise SeqError, "Missing seq_name" if self.seq_name.nil?
+    raise SeqError, "Missing seq"      if self.seq.nil?
+    raise SeqError, "Missing qual"     if self.qual.nil?
+
+    seq_name = self.seq_name
+    seq      = self.seq
+    qual     = self.qual
+
+    "@" + seq_name + $/ + seq + $/ + "+" + $/ + qual + $/
   end
 
   # Method that generates a unique key for a
@@ -227,6 +241,12 @@ class Seq
     end
   end
 
+  # Method to determine the Hamming Distance between
+  # two Sequence objects (case insensitive).
+  def hamming_distance(seq)
+    self.seq.upcase.hamming_distance(seq.seq.upcase)
+  end
+
   # Method that generates a random sequence of a given length and type.
   def generate(length, type)
     raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
@@ -335,7 +355,7 @@ class Seq
   def convert_phred2illumina!
     self.qual.gsub!(/./) do |score|
       score_phred  = score.ord - SCORE_PHRED
-      raise SeqError, "Bad Phred score: #{score} (#{score_phred})" unless (0 .. 40).include? score_phred
+      raise SeqError, "Bad Phred score: #{score} (#{score_phred})" unless (0 .. 41).include? score_phred
       score_illumina = score_phred + SCORE_ILLUMINA
       score          = score_illumina.chr
     end