geneformer restructured + tf binding early version added

Author: janursa

src/methods/geneformer/helper.py.py

@@ -0,0 +1,27 @@
+#!/bin/bash
+#SBATCH --job-name=geneformer
+#SBATCH --output=logs/%j.out
+#SBATCH --error=logs/%j.err
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=20
+#SBATCH --time=25:00:00
+#SBATCH --mem=250GB
+#SBATCH --partition=cpu
+#SBATCH --mail-type=END,FAIL      
+#SBATCH --mail-user=jalil.nourisa@gmail.com   
+
+method="geneformer"
+
+# Import argument parsing functionality
+source "src/utils/parse_args.sh"
+
+# Parse command line arguments
+parse_arguments "$@"
+
+# Pass arguments to Python script
+python_args="--rna $rna --prediction $prediction"
+if [ ! -z "$layer" ]; then
+    python_args="$python_args --layer $layer"
+fi
+
+singularity run ../../images/geneformer python src/methods/${method}/script.py $python_args