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.
It is particularly useful to help evaluate ARGs that have been inferred using tools such as tsinfer, sc2ts, Relate, KwARG, Threads, etc.
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.
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
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.