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.