[Bioperl-l] Bio::Location::Fuzzy CoordinatePolicy questions

Hilmar Lapp hlapp at gmx.net
Thu Sep 7 14:28:16 EDT 2006

I guess there's arguments either way, depending on what you interpret  
the contract to to_FTstring() to be.

If you argue that to_FTstring() needs to return a GenBank feature  
table-compliant string then you cannot leave it to the  
CoordinatePolicy to decide on the end points that satisfy compliance.

Conversely, if you argue that to_FTstring() may return a string which  
is GenBank feature table-compliant only in terms of formatting, then  
there is freedom of interpretation as to what the end points could be.

I'm leaning to the former, as there isn't a universal standard for  
feature location formatting. Or if there is, then this method doesn't  
implement it. It really is there to return a GenBank-compliant  
string. Or so I think - other opinions welcome, and are likely to exist.


On Sep 7, 2006, at 11:04 AM, Chris Fields wrote:

> Hilmar (or whomever can answer this),
> I was looking at a few bug fixes (bug 992 in particular) and  
> noticed that,
> although LocationI-implementing objects are supposed to use a
> CoordinatePolicy for determining start/end coordinates for fuzzy  
> locations,
> Bio::Location::Fuzzy::to_FTstring() does not (it uses max/min_start 
> () and
> max/min_end() instead).  To me, it seems that this should be  
> building the
> location string using the coordinate_policy->start()/end() methods  
> instead
> (as suggested in the bug report).
> The default CoordinatePolicy for Location::Fuzzy is Bio::Location::
> WidestCoordPolicy.
> Would there be any objection to changing this?
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

More information about the Bioperl-l mailing list