[Bioperl-l] Correct values for "strand?"

Chris Dwan (CCGB) cdwan at mail.ahc.umn.edu
Mon Mar 22 12:16:34 EST 2004

There is some debate in my little group of programmers about the correct
values to indicate the strand of a feature.  I'm wondering if there is any
agreed standard that we should work towards...and if (failing that) there
is a preference among the members of this list.

These seem to be the options that I find in the code:

'1' : forward strand (Watson)
'0' : unknown, or not meaninful
'-1' : reverse strand (Crick)

  ** OR **

'+' : forward strand
'-' : reverse strand

I lean towards the first because of the many statements like this
scattered through the code:

  if ($offset = $strand * $frame + $start_pos) { }

It seems to me that the best solution would be an enumerated type with
{ UNKNOWN, FORWARD, REVERSE, MEANINGLESS } ... but that would break a lot
of code.

Any advice is appreciated.

-Chris Dwan
 The University of Minnesota

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