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pybedtools overview and examples

Python wrapper for Aaron Quinlan's BEDtools (http://code.google.com/p/bedtools/).

Note

See http://daler.github.com/pybedtools for the complete documentation

The bedtool object has methods that call the tools in the BEDtools suite. Where appropriate, the method returns another bedtool object, so you can chain or pipe things together just like from the command line. There are also other features not [yet] found in BEDtools like random selection of features, obtaining the centers of features (e.g., for motif detection), reciprocal intersection reports, feature counts, permutation testing, and much more.