Add 3-flank processing variant

downloads-generation/models_class1_processing/GENERATE.sh

@@ -59,18 +59,15 @@ cd $SCRATCH_DIR/$DOWNLOAD_NAME
 export OMP_NUM_THREADS=1
 export PYTHONUNBUFFERED=1
 
-VARIANTS=( with_flanks no_n_flank no_c_flank no_flank )
+VARIANTS=( short_flanks with_flanks no_n_flank no_c_flank no_flank )
 
-if [ "$2" != "continue-incomplete" ]
-then
-    cp $SCRIPT_DIR/generate_hyperparameters.variants.py .
-    cp $SCRIPT_DIR/generate_hyperparameters.base.py .
-    python generate_hyperparameters.base.py > hyperparameters.base.yaml
-    for kind in "${VARIANTS[@]}"
-    do
-        python generate_hyperparameters.variants.py hyperparameters.base.yaml $kind > hyperparameters.$kind.yaml
-    done
-fi
+cp $SCRIPT_DIR/generate_hyperparameters.variants.py .
+cp $SCRIPT_DIR/generate_hyperparameters.base.py .
+python generate_hyperparameters.base.py > hyperparameters.base.yaml
+for kind in "${VARIANTS[@]}"
+do
+    python generate_hyperparameters.variants.py hyperparameters.base.yaml $kind > hyperparameters.$kind.yaml
+done
 
 if [ "$2" == "continue-incomplete" ] && [ -f "hits_with_tpm.csv.bz2" ]
 then

downloads-generation/models_class1_processing/generate_hyperparameters.variants.py

@@ -14,7 +14,7 @@ parser.add_argument(
     help="Production (i.e. standard) hyperparameters grid.")
 parser.add_argument(
     "kind",
-    choices=('with_flanks', 'no_n_flank', 'no_c_flank', 'no_flank'),
+    choices=('with_flanks', 'no_n_flank', 'no_c_flank', 'no_flank', 'short_flanks'),
     help="Hyperameters variant to output")
 
 args = parser.parse_args(argv[1:])
@@ -29,6 +29,9 @@ def transform(kind, hyperparameters):
         new_hyperparameters["n_flank_length"] = 0
     if kind == "no_c_flank" or kind == "no_flank":
         new_hyperparameters["c_flank_length"] = 0
+    if kind == "short_flanks":
+        new_hyperparameters["c_flank_length"] = 3
+        new_hyperparameters["n_flank_length"] = 3
     return [new_hyperparameters]