Skip to main content
Donate to the Python Software Foundation or Purchase a PyCharm License to Benefit the PSF! Donate Now

A class for checking plink bed files

Project description

Description

This is a package for checking plink .bed files (shifted / unshifted):

  • Basic info (number of individual, number of SNPs, etc)
  • Quality control (check whether the shifting is correct)

Requirements

  • Python 3
  • pip3 for installation

Install

Using setup.py

git clone https://github.com/kindlychung/checkbed.git
cd checkbed
python3 setup.py install

Using pip:

From github:

pip3 install --upgrade https://github.com/kindlychung/checkbed.git

or from PyPI:

pip3 install --upgrade checkbed

Usage

You need put your gmail account and password in ~/.pygmailrc, for example:

# suppose the main bed file is xxx.bed
checkcoll xxx
bedinfo xxx

Change log

  • Corrected the collapsed genotype matrix

Project details


Download files

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

Filename, size & hash SHA256 hash help File type Python version Upload date
checkbed-0.2.8.tar.gz (3.9 kB) Copy SHA256 hash SHA256 Source None

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