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

[Chris Fields]

Nice, forgot about those.  Thanks Dan!

chris

On Feb 18, 2010, at 3:20 PM, Dan Kortschak wrote:

> 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
>