[Bioperl-l] Merging overlapping Seq Features

[Cook, Malcolm]

some pointers

http://code.google.com/p/bedtools/
http://genomewiki.ucsc.edu/index.php/Kent_source_utilities such as overlapSelect


Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA
 
 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Chris Fields
> Sent: Thursday, February 18, 2010 10:31 AM
> To: Dan
> Cc: bioperl-l 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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> 
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