[Bioperl-l] option for stupid translation

[Ewan Birney]

On Fri, 19 Oct 2001, Elia Stupka wrote:

> Hi guys,
> 
> before I go ahead and commit, I wanted to check with you, I found that it
> would be useful to have an option on Bio::PrimarySeqI->translate (yes, yet
> another one), which if set to 1 would be passed to Bio::Tools::CodonTable
> in order not to let the codon table "guess" triplets ending in N, i.e not
> using the internal method _translate_ambiguous, but rather just append an
> "X". 

I can see the rationale... but this scares me that we have another option.


What about refactoring so that it takes a hash as the second argument


In the code it goes


   if( ref $arg2 eq "HASH" ) {
      # new stuff
   } else {
      # backward compatibility mode
   }


ewan

  

> 
> The reason? Genscan is not clever enough, and does not translate ambiguous
> triplets, so if something (like the guts of ensembl genscan for example)
> tries to compare the genscan peptide and the bioperl translation, it
> barfs.
> 
> All I want is a optional argument, at the end, which defaults to the usual
> translation.... let me know if I should go ahead and commit on the main
> trunk, then you can have a look at it. ;)
> 
> Elia
> 
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