[Bioperl-l] How to find fuzzy locations?

[Tao Zhu]

Hello, everyone!
In BioPerl HOWTO:Feature-Annotation, Location_Objects
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Location_Objects ,
it says that we could fetch location objects from a SeqFeature::Generic
object like this,
----------------------------------------
      # polyA_signal    1811..1815       
      #                          /gene="NDP"       

   my $start = $feat_object->location->start;       
   my $end = $feat_object->location->end;
----------------------------------------

Location object is a Range object but it has additional capabilities
designed to handle inexact or "fuzzy" locations, where the "start" and
"end" of a particular sub-sequence themselves have start and end
positions, or are not precisely defined. So in the following example we
could still fetch location objects like this,
----------------------------------------
      # polyA_signal    <1811..>1815       

   #             /gene="NDP"       
   my $start = $feat_object->location->start;       
   my $end = $feat_object->location->end;
----------------------------------------
Then we'll get $start=1811 and $end=1815 too.

But how should I do if I just want to exclude such "fuzzy" locations? Is
there any method in BioPerl that could detect such "fuzzy" locations and
then I could exculde them? Thank you!



-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)