liuz-bio/modbamtools

Set of tools to manipulate and visualize modified base bam files

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