bedtools-python
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arq5x
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: [email protected]
=============== bedtools-python
- Requirements
- Cython - sudo easy_install cython
- GNU compiler
- zlib
- 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
- The API
Still need to document this.
- 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
arq5x