Introduction#
What are these lyscripts?#
This package provides convenient scripts for performing inference and learning regarding the lymphatic spread of head & neck cancer. Essentially, it provides a command line interface (CLI) to the lymph library and the lydata repository that stores lymphatic progression data.
We are making these “convenience” scripts public, because doing so is one necessary requirement to making our research easily and fully reproducible. There exists another repository, lynference, where we stored the pipelines that produced our published results in a persistent way.
Installation#
These scripts can be installed via pip:
pip install lyscripts
or installed from source by cloning this repo
git clone https://github.com/lycosystem/lyscripts.git
cd lyscripts
pip install .
Usage#
This package is intended to be mainly used as a collection of Python scripts that would be scattered throughout my projects, if I didn’t bundle them here. Hence, they’re mostly command line tools that do basic and repetitive stuff.
As a Command Line Tool#
Simply run
lyscripts --help
in your terminal to display the help text for the main command. It will list all subcommands that are avialable, which you can then also call with lyscripts <subcommand> --help to get more information on its use and the available arguments.
For example, one subcommand is lyscripts data collect, which will launch a small web server that allows a user to enter patient records on lymphatic involvement in head and neck cancer one row at a time and construct a standardized CSV file from it.