https://github.com/fnl/bceval
BioCreative Evaluation Scripts and Library
https://github.com/fnl/bceval
Last synced: 20 days ago
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BioCreative Evaluation Scripts and Library
- Host: GitHub
- URL: https://github.com/fnl/bceval
- Owner: fnl
- Created: 2011-07-21T13:59:27.000Z (about 15 years ago)
- Default Branch: master
- Last Pushed: 2014-05-19T10:43:39.000Z (about 12 years ago)
- Last Synced: 2025-10-30T18:03:02.694Z (9 months ago)
- Language: Python
- Homepage: www.biocreative.org
- Size: 301 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
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README
Official BioCreative Evaluation Script
**************************************
This package contains the official evaluation script for BioCreative challenges.
It is compatible with Python 2.5-2.7.
It is not compatible with earlier versions of Python.
It has not been tested with Python 3+ and will most likely not work.
Author: Florian Leitner
The BioCreative homepage: http://www.biocreative.org/
General information on the evaluation script: http://www.biocreative.org/resources/biocreative-ii5/evaluation-library/
.. image:: https://zenodo.org/badge/doi/10.5281/zenodo.9970.png
:target: https://zenodo.org/record/9970
:alt: DOI:10.5281/zenodo.9970
Version 3.2
DOI:10.5281/zenodo.9970
============
INSTALLATION
============
Extract the library from the tar.gz::
tar zxvf bc_evaluation-X.X.tar.gz
And move into the created directory::
cd bc_evaluation-X.X.X
Global, system wide installation (you need to have admin/sudo permissions)::
sudo python setup.py install
Local, user-only installation (in your home directory, in "~/.local")::
python setup.py install --user
In case you do a local (user) install, you will have to make sure that the bin directory in "~/.local" is on you PATH, otherwise the bc-evaluate executable will not be found::
export PATH=$PATH:~/.local/bin
To only test if the installation command will work as you think it should, add the option '--dry-run' to the above commands - you will see what will happen, but the setup script will not copy or do anything.
Documentation on installing python packages (using setup.py)::
python setup.py --help
python setup.py --help-commands
python setup.py --help
python setup.py install --help
==================
USAGE INSTRUCTIONS
==================
UNIX, LINUX, OSX
----------------
The installation process should take care that the executable is installed in a way that it can be run from the command-line without further issues. If not, check the last lines when running the script:
copying build/scripts-2.X/bc-evaluate -> /path/to/some/bin
And make sure that path is in your shell's $PATH environment variable. By default, these locations should be:
- Global install: `/usr/local/bin`
- Local user-install: `~/.local/bin`
After installing, you can read instructions on how to use this tool by running its help and documentation commands::
bc-evaluate --documentation
bc-evaluate --help
GENERAL NOTES
-------------
The general way of using this tool is::
bc-evaluate [options] your_result_files... gold_standard_file
The default (w/o options) works for INT/normalizations and results files that have both confidence and rank values, returning a verbose evaluation report. For all other input/output options, please read the --documentation and the --help output carefully.
============
DEPENDENCIES
============
If you want to use the plotting functionality of the script, you need to install matplotlib, a Python plotting library:
http://matplotlib.sourceforge.net/
Matplotlib requires the following external packages:
- python 2.4 (or later, but not python3)
- numpy 1.1 (or later)
- libpng 1.1 (or later)
- freetype 1.4 (or later) [not required to use the plotting functionality of bc-evaluate]
For more information about installing matplotlib, see:
http://matplotlib.sourceforge.net/users/installing.html