This will parse output from
and make a sparse, compressed hdf5 representation for fast queries based on position. Indexing is 1-based and follows the same conventions as samtools's faidx.
Test the package
python setup.py test
then install it into the system package location
pip install .
or, your local path
pip install --user .
from Meth5py import Meth5py
m5 = Meth5py('tests/test_meth.txt', 'tests/test.fa')
for record in m5.fetch('Chr1',10,11):
print(record)
m5.close()Documentation can be found here