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

Fields, Christopher J cjfields at illinois.edu
Thu Jan 19 10:39:42 EST 2012


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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