Bioperl: start, end, strand

[Steve Chervitz]

Ewan Birney writes:
 > 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.
 > 

Some other reasons why we can't rely on start vs. end comparisons to
determine the strand:

1) Single-residue features, (start = end).

2) Circular sequences, (the last base is 5' of the first).

Steve

 > 
 > > 
 > > Brad
 > > 
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