[Bioperl-l] additional methods for Bio::SeqUtils for in-silico cloning

Frank Schwach fs5 at sanger.ac.uk
Fri Jan 20 04:44:33 EST 2012


Hi Russell,

As far as I can see, the previously existing methods 'cat' and 
'trunc_with_features' don't need to deal with circular sequences because 
they wouldn't make biological sense for circular molecules - although 
I'm not sure if it's currently checked whether is_circular is true, 
which we probably should.
For the new methods 'delete', 'insert' and 'ligate' it would make sense 
to use circular molecules as input and it should work except when a 
deletion spans the origin. I currently throw an error when the origin 
would be affected in a circular molecule.

Frank


On 19/01/12 20:45, Smithies, Russell wrote:
> Just to throw a spanner in the works, how do we deal with circular features?
> I'm guessing an "is_circular" flag somewhere then negative cords might be useful?
> Is that what Lincoln did? I think there was a move to allow Gbrowse to handle circular features but don't recall the details.
>
> --Russell
>
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Fields, Christopher J
>> Sent: Friday, 20 January 2012 4:40 a.m.
>> To: Roy Chaudhuri
>> Cc: Frank Schwach;<bioperl-l at bioperl.org>
>> Subject: Re: [Bioperl-l] additional methods for Bio::SeqUtils for in-silico
>> cloning
>>
>> On Jan 19, 2012, at 9:15 AM, Roy Chaudhuri wrote:
>>
>>> I'm not sure I understand the problem with "<1",<  means "less than" not
>> "less than or equal to", so it does not imply that the feature could start at
>> position 1.
>>
>> Yup, that's correct.  My bad.
>>
>>> I can see that there would be cases where negative coordinates might be
>> useful, but I think it is opening a can of worms and could introduce many
>> subtle bugs, so I'd vote for throwing an error. If you were to do it, it would be
>> better to stick with the biological convention of -1 being the base before 1 (as
>> used for -10 and -35 elements).
>>> Roy.
>> Agree with Roy, I think it's best to avoid using negative cords when at all
>> possible, mainly b/c it introduces possibly inconsistent behavior.  Such
>> behavior should be defined in the feature class or its parent class(es),
>> wherever appropriate.  At the moment that doesn't hold true.
>>
>> As a side note, I recall Lincoln allowed negative coords with GBrowse
>> features but I don't recall whether it's officially supported.
>>
>> chris
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