Pybedtools: a flexible Python library for manipulating genomic datasets and annotations by Ryan K. Dale, Brent S. Pedersen and Aaron R. Quinlan.
Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well documented and efficient, and allows researchers to quickly develop simple, yet powerful scripts that enable complex genomic analyses.
From the documentation:
Formats with different coordinate systems (e.g. BED vs GFF) are handled with uniform, well-defined semantics described in the documentation.
Starting to sound like HyTime isn’t it? Transposition between coordinate systems.
If you venture into this area with a topic map, something to keep in mind.
I first saw this in Christophe Lalanne’s A bag of tweets / Dec 2011.