[Bioperl-l] Merging overlapping Seq Features

[Dan]

Great, thanks for the hints.  I've used some of Jim Kent's utilities
before which are very useful.

On Feb 18, 4:45 pm, "Cook, Malcolm" <M... at stowers.org> wrote:
> some pointers
>
> http://code.google.com/p/bedtools/http://genomewiki.ucsc.edu/index.php/Kent_source_utilitiessuch as overlapSelect
>
> Malcolm Cook
> Stowers Institute for Medical Research -  Bioinformatics
> Kansas City, Missouri  USA
>
>
>
>
>
> > -----Original Message-----
> > From: bioperl-l-boun... at lists.open-bio.org
> > [mailto:bioperl-l-boun... at lists.open-bio.org] On Behalf Of
> > Chris Fields
> > Sent: Thursday, February 18, 2010 10:31 AM
> > To: Dan
> > Cc: bioper... at bioperl.org
> > Subject: Re: [Bioperl-l] Merging overlapping Seq Features
>
> > 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
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