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

Chris Fields cjfields at uiuc.edu
Mon Mar 22 15:23:24 EST 2004

The documentation for Bio::SeqFeature::Generic has the optional strand 
settings that you have with values like your first option (1 = forward, -1 
= reverse, 0 = unknown or not meaningful).  I think that those options 
should be enough, unless you think that splitting up the "unknown" and "not 
meaningful" categories would be worth it.  I can't think of anything off 
the top of my head that would be excluded from these categories, although 
I'm sure a few exist.


At 11:16 AM 3/22/2004, Chris Dwan (CCGB) wrote:

>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
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org


Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer


University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
600 S. Mathews Ave.
Urbana, IL 61801

Phone : (217) 333-7098
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