Commit 738f883d authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Update runner

parent d49cbf46
#!/bin/bash #!/bin/bash
# Example script for the INF pipeline # Example script for the INF pipeline
THREADS=12 CORES=12
OUTFOLDER=results OUTFOLDER=results
DATAFOLDER=data DATAFOLDER=data
DATASET=tcga_breast DATASET=tcga_aml
LAYER1=gene LAYER1=gene
LAYER2=cnv LAYER2=meth
TARGET=ER LAYER3=mirna
MODEL=LSVM TARGET=OS
MODEL=randomForest
N_SPLITS_START=0 N_SPLITS_START=0
N_SPLITS_END=10 N_SPLITS_END=10
RANDOM_LABELS=true RANDOM_LABELS=false
# go! # go!
for (( i=$N_SPLITS_START; i<$N_SPLITS_END; i++ )) for (( i=$N_SPLITS_START; i<$N_SPLITS_END; i++ ))
do do
snakemake -s Snakefile_split --cores $THREADS --config datafolder=$DATAFOLDER outfolder=$OUTFOLDER dataset=$DATASET target=$TARGET layer1=$LAYER1 layer2=$LAYER2 model=$MODEL random=$RANDOM_LABELS split_id=$i -p snakemake -s Snakefile_split --cores $CORES --config datafolder=$DATAFOLDER outfolder=$OUTFOLDER dataset=$DATASET target=$TARGET layer1=$LAYER1 layer2=$LAYER2 layer3=$LAYER3 model=$MODEL random=$RANDOM_LABELS split_id=$i -p
done done
if [ $RANDOM_LABELS = true ] if [ $RANDOM_LABELS = true ]
...@@ -29,16 +30,16 @@ fi ...@@ -29,16 +30,16 @@ fi
for MODE in juxt rSNF rSNFi single for MODE in juxt rSNF rSNFi single
do do
python postprocessing/compute_all_metrics.py --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode $MODE python postprocessing/compute_all_metrics.py --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 $LAYER3 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode $MODE
done done
for MODE in juxt rSNF for MODE in juxt rSNF
do do
python postprocessing/borda_global_juxt_rSNF.py --datafolder $DATAFOLDER --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode $MODE python postprocessing/borda_global_juxt_rSNF.py --datafolder $DATAFOLDER --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 $LAYER3 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode $MODE
done done
python postprocessing/borda_global_rSNFi.py --datafolder $DATAFOLDER --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode rSNFi python postprocessing/borda_global_rSNFi.py --datafolder $DATAFOLDER --outfolder $OUTFOLDER --dataset $DATASET --target $TARGET --layers $LAYER1 $LAYER2 $LAYER3 --model $MODEL --n_splits_end $N_SPLITS_END --n_splits_start $N_SPLITS_START --mode rSNFi
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