[Bioperl-l] Transcribe in bioperl

Mark A. Jensen maj at fortinbras.us
Mon Jan 25 08:17:54 EST 2010


transcribe() and rev_transcribe added to Bio::PrimarySeqI, plus tests in 
t/Seq.t, @ r16757
MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>; "Peng Yu" <pengyu.ut at gmail.com>
Sent: Sunday, January 24, 2010 11:39 PM
Subject: Re: [Bioperl-l] Transcribe in bioperl


>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?
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
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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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