https://github.com/kindlychung/checkbed
checkbed, check shifted / collapsed genotype files in plink .bed format
https://github.com/kindlychung/checkbed
Last synced: 4 months ago
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checkbed, check shifted / collapsed genotype files in plink .bed format
- Host: GitHub
- URL: https://github.com/kindlychung/checkbed
- Owner: kindlychung
- Created: 2014-10-31T14:35:58.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2014-10-31T18:51:56.000Z (about 11 years ago)
- Last Synced: 2025-06-04T23:19:21.005Z (7 months ago)
- Language: Python
- Size: 145 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README
Awesome Lists containing this project
README
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