[Bioperl-l] Bioperl-l Digest, Vol 82, Issue 28

[Dan Kortschak]

Hi Dan,

Please try out the BEDTools module included in bioperl-run. It is
currently in BETA, but passes all tests. It interfaces to all the
BEDTools suite.

The returned results from these methods can either be raw bed
descriptions or a variety of BioPerl objects, including sequence
objects.

cheers
Dan

On Thu, 2010-02-18 at 12:00 -0500, bioperl-l-request at lists.open-bio.org
wrote:
> Dan,
> 
> There aren't direct means of doing this beyond asking whether one
> feature contains or overlaps another (not very efficient), or querying
> the a database to find specific overlapping features (much better but
> requires loading the db).  This is something I'm interested in,
> though, both in context with FeatureIO refactors and as a means to
> clean up UCSC's 'every transcript is a gene' issues in GTF
> 
> chris
> 
> On Feb 17, 2010, at 4:04 PM, Dan wrote:
> 
> > Hi, I'm just trying to get to grips with Bioperl as was wondering if
> > anyone could help me accomplish this task: I want to merge together
> > any overlapping sequence features, or features within xbp of each
> > other, that are stored in a BED file.
> > 
> > I have got as far as reading the features in and iterating through
> > them, e.g.:
> > 
> > my $in = Bio::FeatureIO->new(-format => 'bed', -file => "$file");
> > while (my $feat = $in->next_feature) {
> >       print "start: ".$feat->start." end: ".$feat->end."\n";
> > }
> > 
> > Does Bioperl provide anything that could accomplish this merging, or
> > would it be something I would have to write myself?
> > 
> > Any help much appreciated