AIRR-C Deep Dive Tutorial

This page contains resources for the immuneML Deep Dive Tutorial at the AIRR Community Meeting VII.

Downloadable files:

• SillyEncoder.py

• SillyClassifier.py

• silly_ml.yaml

• BrokenOneHotEncoder.py

• BrokenLogisticRegression.py

Commands shown in slides:

All commands are run from the project base folder.

Running check_new_encoder.py

python3 scripts/check_new_encoder.py -h

python3 scripts/check_new_encoder.py -e ./immuneML/encodings/silly/SillyEncoder.py -d sequence -p

Running check_new_ml_method.py

python3 scripts/check_new_ml_method.py -h

python3 scripts/check_new_ml_method.py -m ./immuneML/ml_methods/classifiers/SillyClassifier.py -p

Adding current working dir to PYTHONPATH and running ImmuneMLApp:

export PYTHONPATH="./:$PYTHONPATH"

python3 immuneML/app/ImmuneMLApp.py -h

python3 immuneML/app/ImmuneMLApp.py silly_ml.yaml results/