bw-merge-window 0.2.0

A python extension for quick access to bigWig and bigBed files.

bw-merge-window

A command-line utility for merging and averaging a window of a set of bigWigs, inspired by/tested against the previous C3G bigWigMergePlus tool developed by Romain Grégoire.

This is part of the core set of tools that powers the EpiVar Browser.

Requires: Python 3.10+

License

Everything in this repository EXCEPT FOR EVERYTHING under the tests/bin and tests/data directories is licensed under the terms of the GNU General Public License, v3.0.

© McGill University 2023

Everything under the tests/bin directory is © UCSC. Everything under the tests/data directory is from the IHEC Epigenomes portal and the copyright is retained by the relevant holders.

Installation

pip install bw-merge-window

Usage

bw-merge-window chr1:100000-200000 file1.bw file2.bw --output average.bw [--range 0-1000] [--treat-missing-as-zero]

If the optional flag --treat-missing-as-zero is passed, N/A values in bigWigs become 0, and any 0-values in the merged file will not be written. Otherwise, if a value is missing in one or more of the files, it'll be missing in the merged file as well. This flag is required if you want full backwards-compatibility with bigWigMergePlus.

If you want to include a negative value for --range, use "equals" syntax instead, e.g., --range='-500-1000'.