A project for handling fiber-seq data.
Project description
fibertools
A python package for handling Fiber-seq data.
Free software: MIT license
Documentation: https://fibertools.readthedocs.io.
Install
pip install fibertools
Features
usage: fibertools [-h] [-t THREADS] [-v] [-V] {bam2bed,add-m6a,add-nucleosomes,model,split,trackhub,bed2d4} ...
positional arguments:
{bam2bed,add-m6a,add-nucleosomes,model,split,trackhub,bed2d4}
Available subcommand for fibertools
bam2bed Extract m6a calls from bam and output bed12.
add-m6a Add m6A tag
add-nucleosomes Add Nucleosome and MSP tags
model Make MSP features
split Split a bed over many output files.
trackhub Make a trackhub from a bed file.
bed2d4 Make a multi-track d4 file from a bed file.
optional arguments:
-h, --help show this help message and exit
-t THREADS, --threads THREADS
n threads to use (default: 1)
-v, --verbose increase logging verbosity (default: False)
-V, --version show program's version number and exit
Add nucleosomes and MSPs to a fibertools-rs m6A bam
Create the model
fibertools add-nucleosomes --input input.bam > model.json
Add nucleosomes with the model:
fibertools add-nucleosomes --input input.bam --model model.json > output.bam
Note that by default the input bam file is read from stdin and the output bam file is written to stdout.
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.1.0 (2022-05-01)
First release on PyPI.
Release history Release notifications | RSS feed
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