[Bioperl-l] Merging overlapping Seq Features

[Dan]

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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[Chris Fields]

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

[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

[Noll, Aaron]

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

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

[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...@stowers.org> wrote:
> some pointers
>

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

> > > Bioper...@lists.open-bio.org

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