A set of tools to manipulate and visualize data from base modification bam files
Project description
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
modbamtools-0.4.2.tar.gz
(18.8 kB
view hashes)
Built Distribution
Close
Hashes for modbamtools-0.4.2-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ee93bcc3c93668be8156042426cdb55fceb08fe40b842f76340998642e35711f |
|
MD5 | 663ced789c108fc345cb41c3b1f0b556 |
|
BLAKE2b-256 | 1767c59cbc8d4b697e1cbb1611f5f7c4ce90fe70162463cdacf2ecbbf114ad27 |