[BioRuby] restriction enzyme module

[Trevor Wennblom]

On Apr 5, 2007, at 9:55 AM, Toshiaki Katayama wrote:

>
> I'll forward the patch I sent to you.
> Do you think this is applicable?


Looks good to me, patch applied.  Now how about taking care of AA:

     def to_re(seq)
       str = seq.to_s.upcase
       str.gsub!(/[^BZACDEFGHIKLMNPQRSTVWYU]/, ".")
       str.gsub!("B", "[DN]")
       str.gsub!("Z", "[EQ]")
       Regexp.new(str)
     end

What if we changed it to:

     def to_re(seq)
       str = seq.to_s.upcase
       str.gsub!(/[^BZACDEFGHIKLMNPQRSTVWYU]/, ".")
       str.gsub!("B", "[BDN]")
       str.gsub!("Z", "[ZEQ]")
       str.gsub!("J", "[JIL]")
       Regexp.new(str)
     end

Note i've added Xle to the list.


Trevor