- Project
bedtools-python
- Version
0.1.0
- Authors
- Aaron Quinlan, University of Virginia
- Brent Pedersen, University of California, Berkeley
- Contact
- 1. Cython
- sudo easy_install cython
- GNU compiler
- zlib
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.pyStill need to document this.
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