Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

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

Project description

Meth5py

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.

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for Meth5py, version 0.4.2
Filename, size File type Python version Upload date Hashes
Filename, size Meth5py-0.4.2-py2-none-any.whl (6.9 kB) File type Wheel Python version py2 Upload date Hashes View hashes
Filename, size Meth5py-0.4.2-py3-none-any.whl (6.6 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size Meth5py-0.4.2.tar.gz (5.4 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page