# tsbrowse
Inspect large genetic genealogies (e.g. ARGs) stored in the [tskit](https://tskit.dev) "succinct tree sequence" format, via a web app.
_Tsbrowse_ can scale to ARGs with millions of samples.
It is particularly useful to help evaluate ARGs that have been inferred using tools such as
[tsinfer](https://github.com/tskit-dev/tsinfer),
[sc2ts](https://github.com/tskit-dev/sc2ts),
[Relate](https://github.com/MyersGroup/relate),
[KwARG](https://github.com/a-ignatieva/kwarg),
[Threads](https://pypi.org/project/threads-arg/), etc.
## Quickstart
First install `tsbrowse` from PyPI:
`python -m pip install tsbrowse`
A tskit tree sequence must first be preprocessed to a `.tsbrowse` file:
`python -m tsbrowse preprocess /path/to/trees-file`
This will write a `.tsbrowse` file that can then be viewed using the web app:
`python -m tsbrowse serve /path/to/tsbrowse-file`
This command will launch a web server that can be accessed at `http://localhost:8080` in a web browser.
To display the genes track use:
`python -m tsbrowse serve /path/to/tsbrowse-file --annotations-file genes.`
(where `genes.csv` is a semicolon-separated text file containing no header and information about one gene on a row in the order: `chr;start;end;strand;ensembl ID;gene name`)
An example tree sequence file can be found here: [example.trees](https://raw.githubusercontent.com/tskit-dev/tsbrowse/refs/heads/main/example/example.trees.tsz).
## Tips
If you are using Windows Subsystem for Linux (WSL) you may need to disable Numba's CUDA support:
`NUMBA_DISABLE_CUDA=1 python -m tsbrowse serve /path/to/tsbrowse-file`
A PNG of a specific page in tsbrowse can be generated using the `screenshot` command:
`python -m tsbrowse screenshot /path/to/tsbrowse-file mutations`
## Development
Test are run with pytest:
`python -m pytest`
To run the UI tests so you can see what the browser is doing use
`python -m pytest --headed --slowmo 1000 tests/test_ui.py`
`playwright codegen` is also useful for writing UI test code.
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"description": "# tsbrowse\nInspect large genetic genealogies (e.g. ARGs) stored in the [tskit](https://tskit.dev) \"succinct tree sequence\" format, via a web app.\n_Tsbrowse_ can scale to ARGs with millions of samples.\n\nIt is particularly useful to help evaluate ARGs that have been inferred using tools such as\n[tsinfer](https://github.com/tskit-dev/tsinfer),\n[sc2ts](https://github.com/tskit-dev/sc2ts),\n[Relate](https://github.com/MyersGroup/relate),\n[KwARG](https://github.com/a-ignatieva/kwarg),\n[Threads](https://pypi.org/project/threads-arg/), etc.\n\n## Quickstart\n\nFirst install `tsbrowse` from PyPI:\n\n`python -m pip install tsbrowse`\n\nA tskit tree sequence must first be preprocessed to a `.tsbrowse` file:\n\n`python -m tsbrowse preprocess /path/to/trees-file`\n\nThis will write a `.tsbrowse` file that can then be viewed using the web app:\n\n`python -m tsbrowse serve /path/to/tsbrowse-file`\n\nThis command will launch a web server that can be accessed at `http://localhost:8080` in a web browser.\n\nTo display the genes track use:\n\n`python -m tsbrowse serve /path/to/tsbrowse-file --annotations-file genes.`\n\n(where `genes.csv` is a semicolon-separated text file containing no header and information about one gene on a row in the order: `chr;start;end;strand;ensembl ID;gene name`)\n\nAn example tree sequence file can be found here: [example.trees](https://raw.githubusercontent.com/tskit-dev/tsbrowse/refs/heads/main/example/example.trees.tsz).\n\n## Tips\n\nIf you are using Windows Subsystem for Linux (WSL) you may need to disable Numba's CUDA support:\n\n`NUMBA_DISABLE_CUDA=1 python -m tsbrowse serve /path/to/tsbrowse-file`\n\nA PNG of a specific page in tsbrowse can be generated using the `screenshot` command:\n\n`python -m tsbrowse screenshot /path/to/tsbrowse-file mutations`\n\n\n## Development\n\nTest are run with pytest:\n\n`python -m pytest`\n\nTo run the UI tests so you can see what the browser is doing use\n\n`python -m pytest --headed --slowmo 1000 tests/test_ui.py`\n\n`playwright codegen` is also useful for writing UI test code.\n",
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