There are plenty of tools to do this already, such as bed tools; you can use pybedtools (python wrapper for bedtools) and perform the comparisons in ipython. While not using Perl, pybedtools will allow you to compare multiple BED files at the same time (i.e., more than 2), and is both fast and simple to use. While what you are trying to do isn't bad, there are better tools for the job.

Bioinformatics

In reply to Re: output the overlapping regions to new file by bioinformatics
in thread output the overlapping regions to new file by Anonymous Monk

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