Re: [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-...@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

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[Dan Kortschak]

Hi Malcolm,

It is not entirely obvious where the Kent utilities are available from
the genome wiki page (I can find a closed svn repo with the source, but
no other sites). Would you point me to a download site?

thanks
Dan Kortschak

On Thu, 2010-02-18 at 12:00 -0500, bioperl-...@lists.open-bio.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

[Chris Fields]

Nice, forgot about those. Thanks Dan!

chris

[Smithies, Russell]

http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

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[Cook, Malcolm]

Sure, Dan:

get yer exes here: http://hgdownload.cse.ucsc.edu/admin/exe/

or,

buildit yerself: http://hgdownload.cse.ucsc.edu/downloads.html

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

> -----Original Message-----
> From: Dan Kortschak [mailto:dan.ko...@adelaide.edu.au]
> Sent: Thursday, February 18, 2010 3:43 PM
> To: Cook, Malcolm
> Cc: biop...@lists.open-bio.org