Pepline for IEDB Next-Generation Tools T Cell Class I

Designed by qinti in 20241012

Prerequisites

• Linux 64-bit environment
  • http://www.ubuntu.com/
    • This distribution has been tested on Linux/Ubuntu 64 bit system.
• Python 3.8 or higher
  • http://www.python.org/
• tcsh
  • http://www.tcsh.org/Welcome
    • Under ubuntu: sudo apt-get install tcsh
• gawk
  • http://www.gnu.org/software/gawk/
    • Under ubuntu: sudo apt-get install gawk

Downloading from IEDB website

Installation

tar -xvzf IEDB_NG_TC1-VERSION.tar.gz
mamba create -n IEDB python=3.10
mamba activate IEDB
pip install -r requirements.txt -i https://mirrors.zju.edu.cn/pypi/web/simple
PIP_CONSTRAINTS=pip_constraints.txt pip install -r requirements.txt
pip install numpy==1.24.4

Easy-usage

Step1

python fasta_to_json.py input_sequence.fasta output.json

Step2

python3 src/tcell_mhci.py -j output.json --split --split-dir="./test/"

Step3

python IEDB_predict.py job_descriptions.json