[Bioperl-l] Transcribe in bioperl

Mark A. Jensen maj at fortinbras.us
Sun Jan 24 21:48:33 EST 2010


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?
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> --
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> http://fungalgenomes.org/
>> http://twitter.com/hyphaltip
>>
>>
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