[Bioperl-l] Transcribe in bioperl

Chris Fields cjfields at illinois.edu
Sun Jan 24 23:39:43 EST 2010


I think the main reason there hasn't been a transcribe() is that very few users ask for it.  Most just use a quick '$seq =~ tr/T/U/', or use spliced_seq() and/or translate() (i.e. they don't care about the intermediate mRNA).  I don't have a problem with adding a transcribe method to PrimarySeq, but (and Mark has already picked up on this) it should be constrained to DNA only and return RNA.  And there might be a case for adding the analogous reverse_translate().  

Also worth adding this to the proper interface class (PrimarySeqI, I think) so all Seq/PrimarySeq will have it (or have to implement their own).

chris

On Jan 24, 2010, at 8:48 PM, Mark A. Jensen wrote:

> Not a bad idea, a semantics-preserving/checking thing. transcribe() could return an object with alphabet == 'rna'
> and the T's flipped, or bork if called against an object with alphbet != 'dna'.
> I can add such a thing to Bio::PrimarySeqI (where all these doodads seem to be stashed), if desired.
> 
> ----- Original Message ----- From: "Peng Yu" <pengyu.ut at gmail.com>
> To: "Jason Stajich" <jason at bioperl.org>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Sunday, January 24, 2010 9:22 PM
> Subject: Re: [Bioperl-l] Transcribe in bioperl
> 
> 
>> To convert from T to U. I could use perl's builtin function. But it is
>> semantically far away from 'transcribe'. If there is a function with
>> name 'transcribe', it will be better.
>> On Sun, Jan 24, 2010 at 8:06 PM, Jason Stajich <jason at bioperl.org> wrote:
>>> What exactly do you want to do?
>>> spliced_seq for a feature would be the closest thing...
>>> 
>>> -jason
>>> On Jan 24, 2010, at 5:29 PM, Peng Yu wrote:
>>> 
>>>> I found the function 'translate' in bioperl. But I don't find
>>>> 'transcribe'. Is there such a function?
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>>> --
>>> Jason Stajich
>>> jason.stajich at gmail.com
>>> jason at bioperl.org
>>> http://fungalgenomes.org/
>>> http://twitter.com/hyphaltip
>>> 
>>> 
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