Commit 39c960ce authored by Matthias Bernt's avatar Matthias Bernt
Browse files

restore scripts/run-all-publication-cases.sh

parent 39067ba7
#!/usr/bin/env bash
# This script needs to be run from the deepFPlearn directory.
# Importantly, the conda environment needs to be set up and activated! For certain machines/HPC,
# we have a batch-job that does exactly that and then calls this file
function log_error() {
echo "$@" 1>&2
}
function call_convert() {
if [ -d "$1" ]; then
python -m dfpl convert -f "$1"
else
log_error "Could not find directory for data conversion $1"
fi
}
function call_train() {
if [ -f "$1" ]; then
python -m dfpl train -f "$1"
else
log_error "Could not find training file $1"
fi
}
function call_predict() {
if [ -f "$1" ]; then
python -m dfpl predict -f "$1"
else
log_error "Could not find prediction file $1"
fi
}
#call_train "deepFPlearn_TRAINING/case_00/train_AE_D.json"
#call_train "deepFPlearn_TRAINING/case_00/train_AE_D_full.json"
call_train "deepFPlearn_TRAINING/case_00/train_AE_S.json"
call_train "deepFPlearn_TRAINING/case_00/train_AE_S_full.json"
call_train "deepFPlearn_TRAINING/case_00/train_AE_Sider_full.json"
call_train "deepFPlearn_TRAINING/case_00/train_AE_Tox21_full.json"
call_train "deepFPlearn_TRAINING/case_01/train.json"
call_train "deepFPlearn_TRAINING/case_02/train.json"
call_train "deepFPlearn_TRAINING/case_03/train.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D-AR.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D-ER.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D-ED.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D-GR.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D-TR.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D-PPARg.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D-Aromatase.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D_uncompressed-AR.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D_uncompressed-ER.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D_uncompressed-ED.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D_uncompressed-GR.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D_uncompressed-TR.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D_uncompressed-PPARg.json"
call_predict "deepFPlearn_TRAINING/case_04/predict_D_uncompressed-Aromatase.json"
call_train "deepFPlearn_TRAINING/case_sider/train_SIDER.json"
call_train "deepFPlearn_TRAINING/case_sider/train_SIDER-AE_D.json"
call_train "deepFPlearn_TRAINING/case_sider/train_SIDER-AE_Sider.json"
call_train "deepFPlearn_TRAINING/case_tox21/train_Tox21.json"
call_train "deepFPlearn_TRAINING/case_tox21/train_Tox21-AE_D.json"
call_train "deepFPlearn_TRAINING/case_tox21/train_Tox21-AE_Tox21.json"
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