A set of tools to manipulate and visualize data from base modification bam files
For full documentation and tutorials visit https://rrazaghi.github.io/modbamtools/
Installation
Required: Python 3.8
In a clean environment:
$ pip install modbamtools
Usage
General commands:
Usage: modbamtools [OPTIONS] COMMAND [ARGS]...
A set of tools to manipulate and visualize data from base modification bam
files
Options:
--version Show the version and exit. [default: False]
--help Show this message and exit. [default: False]
Commands:
calcHet Calculate heterogeneity of modified bases for regions in a...
calcMeth Calculate methylation statistics for regions in a bed file
cluster Calculate clustering statistics for regions in a bed file
plot Plot single-read base modification data
Development
To contribute to this tool, first checkout the code. Then create a new virtual environment:
cd modbamtools
python -m venv venv
source venv/bin/activate
Or if you are using pipenv:
pipenv shell
Now install the dependencies and test dependencies:
pip install -e '.[test]'
To run the tests:
pytest