[Bioperl-l] option for stupid translation

Elia Stupka elia@ebi.ac.uk
Fri, 19 Oct 2001 05:56:31 +0100 (BST)

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

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

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. ;)


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