Meth5py 0.4.2

A class for converting BSMAPz methratio output into a fast and compressed hdf5 format

Meth5py

This will parse output from

• BSMAP's methratio.py
• BSMAPz's methratio.py

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.

Installation

Test the package

python setup.py test

then install it into the system package location

pip install .

or, your local path

pip install --user .

Usage

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

Documentation can be found here