[Bioperl-l] Merging overlapping Seq Features

[Noll, Aaron]

Also galaxy has some tools if you download their open source python code.

http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy


On 2/18/10 10:45 AM, "Cook, Malcolm" <MEC at stowers.org> wrote:

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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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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