Bioperl: start, end, strand

[Ewan Birney]

On Tue, 13 Jun 2000, Bradley Marshall wrote:

> 
> In game, the minus strand is handled implicitly if the
> start is larger than the end.  Should I maintain this
> convention in bioperl or explicitly switch the coord's
> and set the strand to -1?


No... 

Bioperl has a strong convention of

	start is *strictly* less than end

and

	strand is one of 1,-1,0 (0 being not strand specific, eg, low
complexity repeat or a variation).


Although start > end => reverse strand is sometimes useful you both

	(a) have difficult in expressing strand 0 type features

	(b) end up with just as many times that you need to reverse
the coordinates as in the case where start is strictly less than end.




> 
> Brad
> 
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