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tsbrowse\n[![License](https://img.shields.io/github/license/tskit-dev/tsbrowse)](https://github.com/tskit-dev/tsbrowse/blob/main/LICENSE) [![PyPI version](https://img.shields.io/pypi/v/tsbrowse.svg)](https://pypi.org/project/tsbrowse/) [![Supported Python Versions](https://img.shields.io/pypi/pyversions/tsbrowse.svg)](https://pypi.org/project/tsbrowse/) [![Docs Build](https://github.com/tskit-dev/tsbrowse/actions/workflows/docs.yml/badge.svg)](https://github.com/tskit-dev/tsbrowse/actions/workflows/docs.yml) [![Tests](https://github.com/tskit-dev/tsbrowse/actions/workflows/tests.yml/badge.svg)](https://github.com/tskit-dev/tsbrowse/actions/workflows/tests.yml)\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\nDocumentation: https://tskit.dev/tsbrowse/docs/stable/ (latest: https://tskit.dev/tsbrowse/docs/latest/)\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/jeromekelleher/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\n## Installation\n\nInstall from PyPI:\n\n```\npython -m pip install tsbrowse\n```\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.csv`\n\n(where `genes.csv` is a semicolon-separated text file containing a header and information about one gene per 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\nTests 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","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftskit-dev%2Ftsbrowse","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftskit-dev%2Ftsbrowse","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftskit-dev%2Ftsbrowse/lists"}