brentp / bedtools-python

A Python interface to the BEDTools API using Cython

Project:	bedtools-python
Version:	0.1.0
Authors:	Aaron Quinlan, University of Virginia Brent Pedersen, University of California, Berkeley
Contact:	[e-mail]

bedtools-python

1. Requirements

1. Cython

• sudo easy_install cython

2. GNU compiler
3. zlib

2. Installation

python setup.py install
./test.sh
# Try it out
examples/ex0-echo.py
examples/ex1-intersect.py
examples/ex2-pysam-and-bedtools.py
examples/ex3-fasta-from-bed.py
examples/ex4-window.py

3. The API

Still need to document this.

4. Examples

Below is a brief example to whet your appetite. For more details on how to use the API, check out the examples/ directory.

>>> from bedtools import IntervalFile
>>>
>>>
>>> exons = IntervalFile("bedtools/tests/data/exons.hg18.chr21.bed")
>>> rmsk  = IntervalFile("bedtools/tests/data/rmsk.hg18.chr21.bed")
>>>
>>> # find exons that overlap with repeat annotations
>>> ex = exons.next()
>>> for hit in rmsk.search(ex):
...      print ex.chrom,  ex.start,  ex.end,\
...            hit.chrom, hit.start, hit.end,
chr21 9928613 9928911 chr21 9928614 9928678