[BioPython] Translation issues

[Renato Alves]

Peter wrote:
> Sadly, that is the just way the translation module works.  This is a
> fairly common problem, and its one I was planning to try and "fix" as
> part of Bug 2382
> http://bugzilla.open-bio.org/show_bug.cgi?id=2381
>   
In this case, I guess that something that tests if the 1st codon is a 
start codon and matches the codon table's start codons, would be 
replaced by "M". But this is a very naive and specific thing. I don't 
know if this could break other uses of this function.
> I would like some comments on the ideas on that bug - for example
> would you prefer separate methods/functions for blind translation,
> translation until a stop codon, and translation from a start codon
> which is treated as an M - or a single method with lots of optional
> arguments?
>   
I don't have the expertise to distinguish the pros and cons between the 
two approaches.
Still, in terms of potential user friendliness, I would go for separate 
methods/functions to keep the task simple and obvious.
> Right now, I would check the start codon yourself and then use an M
> when translating the sequence.  Remember the codon table (table 11 in
> your example) should have all the valid start codons defined.
>   
I'm adopting the technique suggested by Bruce Southey to workaround this 
particular problem. Still this wouldn't work on more elaborate cases 
like some of the ones described on the bug thread you mentioned.

Still, many thanks for the quick and clean answers.

Renato