Population Coverage tool - version 3.0.2 ========================================== Release Note ------------ 2020-05-12 * This release will run only under Python 3.6 or higher. Prerequisites: ------------- + Python 3.6 or higher * http://www.python.org/ + numpy * https://pypi.python.org/pypi/numpy - Under ubuntu: pip install numpy==1.19.5 - Python 3.10 or higher: pip install numpy==1.24.2 + matplotlib * https://matplotlib.org/downloads.html - Under ubuntu: pip install matplotlib==2.0.0 - Python 3.10 or higher: pip install matplotlib==3.7.0 Installation: ------------ Unpack the tar.gz files (IEDB_Population_Coverage-3.0.2.tar.gz) Run the 'configure' script to install necessary packages and requirements file. Specifically for population_coverage $ tar -zxvf IEDB_Population_Coverage-3.0.2.tar.gz $ cd population_coverage $ ./configure Usage: ----- * Display usage $ python calculate_population_coverage.py --help * List all populations $ python calculate_population_coverage.py --list * Calculate population coverage for a given file containing epitope sequence and a list of alleles. $ python calculate_population_coverage.py -p -c -f Example: $ python calculate_population_coverage.py -p Japan -c I -f ./test/mhci_alleles.txt * Calculate population coverage and generate plots. $ python calculate_population_coverage.py -p -c -f --plot Example: $ python calculate_population_coverage.py -p Japan -c II -f ./test/mhcii_alleles.txt --plot test