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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


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Files for checkbed, version 0.2.8
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