smoothed ruby code to get rid of warnings

[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 3b950aef6c3ae6326b65d4a2217f0eef4d672976..9eb4fbf76538273897cf65bf9657df6a47794b01 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
@@ -45,7 +46,18 @@ class Seq
 
   attr_accessor :seq_name, :seq, :type, :qual
 
-  # Method that generates all possible oligos of a specifed length and type.
+  # Class method to instantiate a new Sequence object given
+  # a Biopiece record.
+  def self.new_bp(record)
+    seq_name = record[:SEQ_NAME]
+    seq      = record[:SEQ]
+    type     = record[:SEQ_TYPE]
+    qual     = record[:SCORES]
+
+    self.new(seq_name, seq, type, qual)
+  end
+
+  # Class method that generates all possible oligos of a specifed length and type.
   def self.generate_oligos(length, type)
     raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
 
@@ -167,18 +179,31 @@ class Seq
     raise SeqError, "Missing seq_name" if self.seq_name.nil?
     raise SeqError, "Missing seq"      if self.seq.nil?
 
-    seq_name = self.seq_name
-    seq      = self.seq
+    seq_name = self.seq_name.to_s
+    seq      = self.seq.to_s
 
     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.to_s
+    seq      = self.seq.to_s
+    qual     = self.qual.to_s
+
+    "@" + seq_name + $/ + seq + $/ + "+" + $/ + qual + $/
   end
 
   # Method that generates a unique key for a
@@ -227,6 +252,12 @@ 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