[Bioperl-l] Re: translation using Bioperl

[hilmar.lapp@pharma.Novartis.com]

Add one more optional, boolean argument, $fullCDS, to method
translate.
If it is true:

1. Check and replace the initial amino acid.

2. Remove the trailing stop character
   Note that this is the default behaviour now. In my opinion ,
   the trailing stops should be left there by default.

3. Warn if a) first codon is not a valid initiator
           b) last codon is not a stop


Comments anyone?

     -Heikki

   At first glance, sounds okay except for the last point. My comments are
   1) If you can put up rules having certain consequences, that is, if
   there is a contract, and the rules are not met, this is an exception.
   So, don't warn, but throw an exception. I wonder how you want to catch a
   warning programmatically and react upon it properly.
   2) The conditions you are mentioning in 3) sound like a validation. So,
   one (the user) might like to validate whether a given sequence could be
   a full CDS. If a sequence does not pass this validation, translate()
   with $fullCDS == 1 should throw an exception. The validation may be even
   a method offered by a module other than PrimarySeqI, maybe even
   CodonTable, but that's just a first guess.

      Hilmar