[Bioperl-l] option for stupid translation

[Heikki Lehvaslaiho]

Elia,

Did you notice that CodonTable has a method translate_strict()?
Go ahead and commit.

	-Heikki


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".
> 
> 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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______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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