[BioRuby-cvs] bioruby/lib/bio/sequence na.rb,1.3,1.4

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv7649/lib/bio/sequence

Modified Files:
	na.rb 
Log Message:
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
are newly added.
Bio::Sequence::NA#gc_percent are changed not to raise ZeroDivisionError
and returns 0 when given sequence is empty.


Index: na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/na.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** na.rb	26 Mar 2006 02:27:59 -0000	1.3
--- na.rb	27 Jun 2006 05:44:57 -0000	1.4
***************
*** 282,286 ****
  
    # Calculate the ratio of GC / ATGC bases as a percentage rounded to 
!   # the nearest whole number.
    #
    #   s = Bio::Sequence::NA.new('atggcgtga')
--- 282,286 ----
  
    # Calculate the ratio of GC / ATGC bases as a percentage rounded to 
!   # the nearest whole number. U is regarded as T.
    #
    #   s = Bio::Sequence::NA.new('atggcgtga')
***************
*** 292,299 ****
--- 292,356 ----
      at = count['a'] + count['t'] + count['u']
      gc = count['g'] + count['c']
+     return 0 if at + gc == 0
      gc = 100 * gc / (at + gc)
      return gc
    end
  
+   # Calculate the ratio of GC / ATGC bases. U is regarded as T.
+   #
+   #   s = Bio::Sequence::NA.new('atggcgtga')
+   #   puts s.gc_content                       #=> 0.555555555555556
+   # ---
+   # *Returns*:: Float
+   def gc_content
+     count = self.composition
+     at = count['a'] + count['t'] + count['u']
+     gc = count['g'] + count['c']
+     return 0.0 if at + gc == 0
+     return (gc.to_f / (at + gc).to_f)
+   end
+ 
+   # Calculate the ratio of AT / ATGC bases. U is regarded as T.
+   #
+   #   s = Bio::Sequence::NA.new('atggcgtga')
+   #   puts s.at_content                       #=> 0.444444444444444
+   # ---
+   # *Returns*:: Float
+   def at_content
+     count = self.composition
+     at = count['a'] + count['t'] + count['u']
+     gc = count['g'] + count['c']
+     return 0.0 if at + gc == 0
+     return (at.to_f / (at + gc).to_f)
+   end
+ 
+   # Calculate the ratio of (G - C) / (G + C) bases.
+   #
+   #   s = Bio::Sequence::NA.new('atggcgtga')
+   #   puts s.gc_skew                          #=> 0.6
+   # ---
+   # *Returns*:: Float
+   def gc_skew
+     count = self.composition
+     g = count['g']
+     c = count['c']
+     return 0.0 if g + c == 0
+     return ((g - c).to_f / (g + c).to_f)
+   end
+ 
+   # Calculate the ratio of (A - T) / (A + T) bases. U is regarded as T.
+   #
+   #   s = Bio::Sequence::NA.new('atgttgttgttc')
+   #   puts s.at_skew                          #=> -0.75
+   # ---
+   # *Returns*:: Float
+   def at_skew
+     count = self.composition
+     a = count['a']
+     t = count['t'] + count['u']
+     return 0.0 if a + t == 0
+     return ((a - t).to_f / (a + t).to_f)
+   end
+ 
    # Returns an alphabetically sorted array of any non-standard bases 
    # (other than 'atgcu').