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. example: chr21:1-1000
-br, --batch PATH makes html/pdf report for all regions in the bed file
-g, --gtf PATH makes gene tracks from sorted and tabix gtf files
-b, --bed PATH makes tracks from sorted and tabix bed files. This
will plot each interval as a rectangle (similar to
gtf)
-bw, --bigwig PATH makes a track from bigwig files
-bd, --bedgraph PATH makes a track from bedgraph files
-s, --samples TEXT sample names per each bam input
-tr, --track-titles TEXT titles of tracks provided in order of gtf files,
bed files, bigwig files, bedgraph files
-hp, --hap reads will be grouped according to HP tag in bam
(comma separated)
-st, --strands reads will be grouped by strand 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. This is for fine tuning, the
height is automatically calculated.
-w, --width INTEGER width of plot in px
--help Show this message and exit.
example: modbamtools plot -br $regions --gtf $gtf --out $out -hp -b $bed -bw $bw1 -bw $bw2 --prefix $prefix --fmt html --samples $names --track-titles $tracks $bam
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
