sequence.rb in parse_fasta-1.7.2

- old
+ new

@@ -18,10 +18,20 @@
 
 # Provide some methods for dealing with common tasks regarding
 # nucleotide sequences.
 class Sequence < String
 
+  # Strips whitespace from the str argument before calling super
+  #
+  # @return [Sequence] A Sequence string
+  #
+  # @example Removes whitespace
+  #   Sequence.new "AA CC TT" #=> "AACCTT"
+  def initialize(str)
+    super(str.gsub(/ +/, ""))
+  end
+
   # Calculates GC content
   #
   # Calculates GC content by dividing count of G + C divided by count
   # of G + C + T + A + U. If there are both T's and U's in the
   # Sequence, things will get weird, but then again, that wouldn't
@@ -43,11 +53,11 @@
     c = s.count('c')
     g = s.count('g')
     t = s.count('t')
     a = s.count('a')
     u = s.count('u')
-    
+
     return 0 if c + g + t + a + u == 0
     return (c + g) / (c + g + t + a + u).to_f
   end
 
   # Returns a map of base counts
@@ -85,13 +95,13 @@
       counts[:u] = u
     elsif t > 0 && u > 0
       warn('ERROR: A sequence contains both T and U')
       counts[:t], counts[:u] = t, u
     end
-    
+
     counts[:n] = s.count('n') if count_ambiguous_bases
-    
+
     counts
   end
 
   # Returns a map of base frequencies
   #
@@ -114,10 +124,10 @@
   #
   # @return [Hash] A hash with base as key, frequency as value
   def base_frequencies(count_ambiguous_bases=nil)
     base_counts = self.base_counts(count_ambiguous_bases)
     total_bases = base_counts.values.reduce(:+).to_f
-    base_freqs = 
+    base_freqs =
       base_counts.map { |base, count| [base, count/total_bases] }.flatten
     Hash[*base_freqs]
   end
 end