IEDB Next-Generation Tools PHBR - version 0.2.2-beta
========================================================================

Introduction
------------
Patient Harmonic-mean Best Rank (PHBR) is a metric that represents how well the HLA genotype of an individual can present a specific mutation.

Release Notes
-------------
v0.2.2-beta - Initial public beta release


Prerequisites
-------------
The following prerequisites must be met before installing this tool:

+ Linux 64-bit environment.  Most modern Linux distributions should work.
  * http://www.ubuntu.com/

+ Python 3.8 or higher
  * http://www.python.org/

+ IEDB T Cell Class I & II Tools
  * https://nextgen-tools-dev.iedb.org/download-all


Installation
------------
Below, we will use the example of installing to ~/iedb_tools.

1. Extract the code and change directory: 
  $ mkdir ~/iedb_tools
  $ tar -xvzf IEDB_NG_PHBR-0.2.2-beta.tar.gz -C ~/iedb_tools
  $ cd ~/iedb_tools/ng_phbr-0.2.2-beta

2. Configure the paths related TC1 and TC2 in the `paths.py` to match the layout of your system.

3. Run the `configure` script:

  $ ./configure

Usage
-----

python3 src/run_phbr.py predict [-j] <input_json_file>

The output format will be 'json'.

1. Running basic example where MHCI-binding must perform.
Example: python3 src/run_phbr.py predict -j examples/mhci-binding-input.json -o output

2. Running basic example where MHCII-binding must perform.
Example: python3 src/run_phbr.py predict -j examples/mhcii-binding-input.json -o output

3. Running basic example where both MHCI-binding and MHCII-binding must perform.
Example: python3 src/run_phbr.py predict -j examples/mhc-combined-binding-input.json -o output

Input formats
-------------
Inputs may be specified in JSON format.  See the JSON files in the 'examples'
directory.

Output formats
--------------
Outputs, by default, will be in TSV format. It may be specified in JSON format
by setting the '--output-format/-f' flag to 'json'.
Example: python3 src/run_phbr.py predict -j examples/mhci-binding-input.json -o output -f json

See the JSON file (example-output.json) in the 'examples' directory.


Caveats
-------
All IEDB next-generation standalones have been developed with the primary
focus of supporting the website.  Some user-facing features may be lacking,
but will be improved as these tools mature.


Contact
-------
Please contact us with any issues encountered or questions about the software
through any of the channels listed below.

IEDB Help Desk: https://help.iedb.org/
Email: help@iedb.org