A set of tools to manipulate and visualize data from base modification bam files
Project description
modbamtools
A set of tools to manipulate and visualize data from base modification bam files
Installation
Install this tool using pip
:
$ 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.
--help Show this message and exit.
Commands:
plot This Command will plot single-read base modification data
Plotting command:
Usage: modbamtools plot [OPTIONS] BAMS...
This Command will plot single-read base modification data
Options:
-r, --region TEXT region of interest (chr21:1-1000) [required]
-g, --gtf PATH gtf file in .gz sorted and tabix [required]
-s, --samples TEXT sample names per each bam input
-hp, --hap Reads will be grouped according to HP tag in bam
-o, --out PATH output path for html plot [required]
-p, --prefix TEXT file name for output
-f, --fmt TEXT format of output file (png, html, svg, pdf)
-u, --can_prob FLOAT probability threshold for canonical bases
-m, --mod_prob FLOAT probability threshold for modified bases
-h, --height INTEGER height of plot in px
-w, --width INTEGER width of plot in px
--help Show this message and exit.
example: modbamtools plot -r chr22:29188081-29222181 -hp --gtf gencode.v38.annotation.sorted.gtf.gz --out ./plots modbam.bam -h 1000
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
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