Inspect large genetic genealogies (e.g. ARGs) stored in the tskit "succinct tree sequence" format, via a web app.
Tsbrowse can scale to ARGs with millions of samples.
Documentation: https://tskit.dev/tsbrowse/docs/stable/ (latest: https://tskit.dev/tsbrowse/docs/latest/)
It is particularly useful to help evaluate ARGs that have been inferred using tools such as tsinfer, sc2ts, Relate, KwARG, Threads, etc.
Install 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.csv
(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)
An example tree sequence file can be found here: example.trees.
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
Tests 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.