Bed Reader
Project description
bed-reader
A simple and efficient PLINK *.bed file format reader and writer.
Read and write genetic PLINK *.bed/bim/fam files. Also, efficiently read parts of files and access metadata.
Documentation
- API Documentation with examples.
- Project Home and Full Annotated Bibliography
Code
Contacts
- Email the developers at fastlmm-dev@python.org.
- Join the user discussion and announcement list (or use web sign up).
- Open an issue on GitHub.
Quick install:
If you have pip installed, installation is as easy as:
pip install bed-reader
Detailed Package Install Instructions:
pysnptools has the following dependencies:
python 3.7 or 3.8 (on MacOS, just 3.7)
Package(s):
- numpy
(1) Installing from source
Go to the directory where you copied the source code for bed-reader
On Linux:
At the shell, type:
sudo python setup.py install
On Windows:
At the OS command prompt, type
python setup.py install
For developers (and also to run regression tests)
pip install -r requirements-dev.txt
When working on the developer version, first add the src directory of the package to your PYTHONPATH environment variable.
To build extension (from .\src dir), type the following at the OS prompt:
python setup.py build_ext --inplace
Don't forget to set your PYTHONPATH to point to the directory above the one named bed-reader in the bed-reader source code. For e.g. if bed-reader is in the [somedir] directory, then in the Unix shell use:
export PYTHONPATH=$PYTHONPATH:[somedir]
Or in the Windows DOS terminal, one can use:
set PYTHONPATH=%PYTHONPATH%;[somedir]
Note for Windows: You must have Visual Studio installed.
Running regression tests
From the directory tests at the top level, run:
pytest
This will run a series of regression tests.
Note that you must use "python setup.py build_ext --inplace" to run the regression tests, and not "python setup.py install".
Project details
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