[Bioperl-l] Merging overlapping Seq Features

Dan dan.halligan at gmail.com
Wed Feb 17 17:04:05 EST 2010

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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