[Bioperl-l] question about in-between overlapping exact location
hartzell at alerce.com
Wed May 6 00:17:49 EDT 2009
Jason Stajich writes:
> George -
> I don't think the location type is taken into account in the overlap
> code testing code. Would you expect 2..3 and 3..5 to overlap?
> On May 5, 2009, at 2:42 PM, George Hartzell wrote:
> > I was surprised to see that:
> > $ins = Bio::Location::Simple->new(-start => 2,
> > -end => 3,
> > -location_type => 'IN-BETWEEN',
> > );
> > $start = Bio::Location::Simple->new(-start => 3,
> > -end => 5);
> > print "Wow!\n" if $start->overlaps($ins);
> > To my mind they would only overlap if the insertion were 3^4 or 4^5.
> > Is my mental model of in-between's overlapping exact's wrong, or could
> > the code be improved (I'm happy to make a change, but...)?
Yep, I'd expect them to overlap.
1 2 3 4 5
T A A
I'm trying to ask a question like the following. Given a location
that describes an e.g. start codon (3..5) and a description of a
mutation, does the mutation cause a change in the ATG. Substitutions
are described with exact locations (change bases 3..4 from AT to TA)
and insertions are modeled as in-between locations (insert G at 3^4).
1 2 3 4 5 6
A T G
T G C C
Given 3..5, I can just ask if 3..4 overlaps it (yes), if 3 overlaps it
(yes) and if 3^4 overlaps it (yes). For things to work out this
easily, 2^3 shouldn't overlap (an insertion there wouldn't change the
I can get the in-between to work by using RangeI->contains, but then I
end up with 1..4 not "causing a change".
I've ended up with a two part if() that checks the location_type and
uses ->overlap() or ->contains() so that it works out.
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