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

Frank Schwach fs5 at sanger.ac.uk
Wed Jan 25 13:08:10 EST 2012


just wanted to say that I have updated Bio::SeqUtils in my git master 
branch so that it now throws an exception if negative coordinates are 
encountered. There is also a bugfix for incorrectly adjusted positions 
following deletions in some situations.
I have made a new pull request to bioperl-live.
Thanks Roy and Chris!

Frank


On 19/01/12 15:44, Frank Schwach wrote:
> ok, then let's throw an error when negative postions are supplied. I'll
> make the changes to the queued pull request.
>
> Cheers,
>
> Frank
>
>
> On 19/01/12 15:39, Fields, Christopher J wrote:
>> 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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