[BioRuby-cvs] bioruby/lib/bio/data na.rb,0.20,0.21

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/data
In directory dev.open-bio.org:/tmp/cvs-serv19921/lib/bio/data

Modified Files:
	na.rb 
Log Message:
Integrate Toshiaki's improvements of to_re in Bio::Sequence::NA

Index: na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/data/na.rb,v
retrieving revision 0.20
retrieving revision 0.21
diff -C2 -d -r0.20 -r0.21
*** na.rb	8 Feb 2006 12:15:42 -0000	0.20
--- na.rb	5 Apr 2007 23:10:09 -0000	0.21
***************
*** 159,165 ****
  
      def to_re(seq, rna = false)
        str = seq.to_s.downcase
        str.gsub!(/[^atgcu]/) { |base|
!         NAMES[base] || '.'
        }
        if rna
--- 159,179 ----
  
      def to_re(seq, rna = false)
+       replace = {
+         'y' => '[tcy]',
+         'r' => '[agr]',
+         'w' => '[atw]',
+         's' => '[gcw]',
+         'k' => '[tgk]',
+         'm' => '[acm]',
+         'b' => '[tgcyskb]',
+         'd' => '[atgrwkd]',
+         'h' => '[atcwmyh]',
+         'v' => '[agcmrsv]',
+         'n' => '[atgcyrwskmbdhvn]'
+       }
+ 
        str = seq.to_s.downcase
        str.gsub!(/[^atgcu]/) { |base|
!         replace[base] || base
        }
        if rna