[Bioperl-l] Re: translation using Bioperl

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Wed, 26 Jul 2000 13:07:46 +0100

Add one more optional, boolean argument, $fullCDS, to method
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?


   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.