File size: 2,029 Bytes
7718235 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 |
#!/bin/bash
# $1 is the name of the scripts folder
# $2 is the name of output folder
# $3 is the gpu ids that used for training, seperated by comma
CUDA_VISIBLE_DEVICES=$3
echo "CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES
for fold in {0..4}
do
for task in $(cat scripts/gene.txt) $(cat scripts/gene.itan.txt) $(cat scripts/gene.large.window.txt) $(cat scripts/gene.pfams.txt); do
echo "Begin "$task" fold "$fold
mkdir $2/$task
# check if task has finished, unless the skip argument is present
logdir=$(cat $1/$task.5fold/$task.fold.$fold.yaml | grep log_dir | sed 's/.*: //')
num_epochs=$(cat $1/$task.5fold/$task.fold.$fold.yaml | grep num_epochs | sed 's/.*: //')
data_file_test=$(cat $1/$task.5fold/$task.fold.$fold.yaml | grep data_file_test: | sed 's/.*: //')
data_file_train=$(cat $1/$task.5fold/$task.fold.$fold.yaml | grep data_file_train: | sed 's/.*: //')
if [ -f $logdir/FOLD.0/model.epoch.$num_epochs.pt ] && [ -f $logdir/FOLD.1/model.epoch.$num_epochs.pt ] && [ -f $logdir/FOLD.2/model.epoch.$num_epochs.pt ] && [ -f $logdir/FOLD.3/model.epoch.$num_epochs.pt ]; then
echo "Begin "$task" fold "$fold
mkdir $2/$task
if [ ! -f $2/$task/testing.fold.$fold.4fold.csv ]; then
python -W ignore::UserWarning:torch_geometric.data.collate:147 train.py \
--conf $1/$task.5fold/$task.fold.$fold.yaml \
--data-file-test $data_file_test \
--mode interpret_4_fold --interpret-by both --out-dir $2/$task/testing.fold.$fold.4fold.csv
fi
if [ ! -f $2/$task/training.fold.$fold.4fold.csv ] && [[ ! $(cat scripts/gene.pfams.txt) == *"$task"* ]]; then
python -W ignore::UserWarning:torch_geometric.data.collate:147 train.py \
--conf $1/$task.5fold/$task.fold.$fold.yaml \
--data-file-test $data_file_train \
--mode interpret_4_fold --interpret-by both --out-dir $2/$task/training.fold.$fold.4fold.csv
fi
else
echo $task" fold "$fold" not finished"
fi
done
done
|