| Name | bw-merge-window JSON |
| Version |
0.2.0
JSON |
| download |
| home_page | |
| Summary | A python extension for quick access to bigWig and bigBed files. |
| upload_time | 2024-01-04 16:11:29 |
| maintainer | |
| docs_url | None |
| author | David Lougheed |
| requires_python | >=3.10,<4.0 |
| license | GPL-3.0 |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
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No Travis.
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# bw-merge-window
[](https://badge.fury.io/py/bw-merge-window)
[](https://codecov.io/gh/c3g/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](https://github.com/c3g/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](./LICENSE).
© 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
```bash
pip install bw-merge-window
```
## Usage
```bash
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'`.
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