tsbrowse 0.0.1

Webapp to view and visualise tskit ARGs

tsbrowse

Inspect large genetic genealogies (e.g. ARGs) stored in the tskit "succinct tree sequence" format, via a genome browser style app. Tsbrowse can deal with ARGs of thousands or potentially 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.

To view a tskit tree sequence or tszip file first pre-process it:

python -m tsbrowse preprocess /path/to/trees-file

This will write a .tsbrowse file

To launch the app use:

python -m tsbrowse serve /path/to/tsbrowse-file

Or to generate a PNG of a specific page use, e.g:

python -m tsbrowse screenshot /path/to/tsbrowse-file mutations

On WSL, it may be necessary to disable Numba's CUDA support:

NUMBA_DISABLE_CUDA=1 python -m tsbrowse serve /path/to/tsbrowse-file

Installation

tsbrowse is currently in development. To install the latest dev version from github, try

python -m pip install git+https://github.com/tskit-dev/tsbrowse

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.