File size: 2,682 Bytes
0b11a42 |
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 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 |
#data_time for hydra output folder
get_data_time(){
date=$(ls outputs/ | head -n 1)
time=$(ls outputs/*/ | head -n 1)
date=$date
time=$time
}
train_model(){
python -m transforna --config-dir="/nfs/home/yat_ldap/VS_Projects/TransfoRNA-Framework/conf"\
model_name=$1 trained_on=$2 num_replicates=$4
get_data_time
#rename the folder to model_name
mv outputs/$date/$time outputs/$date/$3
ls outputs/$date/
rm -rf models/tcga/TransfoRNA_${2^^}/$5/$3
mv -f outputs/$date/$3 models/tcga/TransfoRNA_${2^^}/$5/
rm -rf outputs/
}
#activate transforna environment
eval "$(conda shell.bash hook)"
conda activate transforna
#create the models folder if it does not exist
if [[ ! -d "models/tcga/TransfoRNA_ID/major_class" ]]; then
mkdir -p models/tcga/TransfoRNA_ID/major_class
fi
if [[ ! -d "models/tcga/TransfoRNA_FULL/sub_class" ]]; then
mkdir -p models/tcga/TransfoRNA_FULL/sub_class
fi
if [[ ! -d "models/tcga/TransfoRNA_ID/sub_class" ]]; then
mkdir -p models/tcga/TransfoRNA_ID/sub_class
fi
if [[ ! -d "models/tcga/TransfoRNA_FULL/major_class" ]]; then
mkdir -p models/tcga/TransfoRNA_FULL/major_class
fi
#remove the outputs folder
rm -rf outputs
#define models
models=("seq" "seq-seq" "seq-rev" "seq-struct" "baseline")
models_capitalized=("Seq" "Seq-Seq" "Seq-Rev" "Seq-Struct" "Baseline")
num_replicates=5
############train major_class_hico
##replace clf_target:str = 'sub_class_hico' to clf_target:str = 'major_class_hico' in ../conf/train_model_configs/tcga.py
sed -i "s/clf_target:str = 'sub_class_hico'/clf_target:str = 'major_class_hico'/g" conf/train_model_configs/tcga.py
#print the file content
cat conf/train_model_configs/tcga.py
#loop and train
for i in ${!models[@]}; do
echo "Training model ${models_capitalized[$i]} for id on major_class"
train_model ${models[$i]} id ${models_capitalized[$i]} $num_replicates "major_class"
echo "Training model ${models[$i]} for full on major_class"
train_model ${models[$i]} full ${models_capitalized[$i]} 1 "major_class"
done
############train sub_class_hico
#replace clf_target:str = 'major_class_hico' to clf_target:str = 'sub_class_hico' in ../conf/train_model_configs/tcga.py
sed -i "s/clf_target:str = 'major_class_hico'/clf_target:str = 'sub_class_hico'/g" conf/train_model_configs/tcga.py
for i in ${!models[@]}; do
echo "Training model ${models_capitalized[$i]} for id on sub_class"
train_model ${models[$i]} id ${models_capitalized[$i]} $num_replicates "sub_class"
echo "Training model ${models[$i]} for full on sub_class"
train_model ${models[$i]} full ${models_capitalized[$i]} 1 "sub_class"
done
|