[Bioperl-l] Merging overlapping Seq Features

Chris Fields cjfields at illinois.edu
Thu Feb 18 11:31:23 EST 2010


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


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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