single omics methods receive arguments

runs.ipynb

@@ -81,7 +81,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -182,6 +182,71 @@
     "#         subprocess.run(command, shell=True, check=True)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Run grn inference "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted batch job 7748321\n"
+     ]
+    }
+   ],
+   "source": [
+    "par = {\n",
+    "    # 'methods': ['pearson_corr', 'portia', 'grnboost2', 'ppcor', 'scenic', 'scglue', 'celloracle'],\n",
+    "    'methods': ['ppcor'],\n",
+    "    'write_dir': 'resources/grn_models/',\n",
+    "    'multiomics_rna': 'resources/grn-benchmark/multiomics_rna.h5ad',\n",
+    "    'num_workers': 20,\n",
+    "    'mem': \"100G\",\n",
+    "    'time': \"24:00:00\"\n",
+    "}\n",
+    "for method in par['methods']:\n",
+    "    par['prediction'] = f\"{par['write_dir']}/{method}.csv\"\n",
+    "    # method arguments \n",
+    "    method_args=f\"--multiomics_rna {par['multiomics_rna']} --prediction {par['prediction']} --num_workers  {par['num_workers']}\"\n",
+    "    # run command\n",
+    "    if method == \"pearson_corr\":\n",
+    "        command = f\"python src/control_methods/pearson/script.py {method_args}\"\n",
+    "    elif method == \"celloracle\":\n",
+    "        command = f\"/home/jnourisa/miniconda3/envs/celloracle/bin/python src/methods/multi_omics/celloracle/script.py {method_args}\"\n",
+    "    elif method in [\"grnboost2\", \"scenic\", \"genie3\"]:\n",
+    "        command = f\"singularity exec ../../images/scenic python src/methods/single_omics/{method}/script.py {method_args}\" \n",
+    "    elif method == 'scglue':\n",
+    "        command = f\"singularity exec ../../images/scglue python src/methods/multi_omics/{method}/script.py {method_args}\"\n",
+    "    elif method == 'ppcor':\n",
+    "        command = f\"singularity exec ../../images/ppcor Rscript src/methods/single_omics/{method}/script.R {method_args}\"\n",
+    "    else:\n",
+    "        command = f\"singularity exec ../../images/{method} python src/methods/single_omics/{method}/script.py {method_args}\"\n",
+    "    # sbatch tags\n",
+    "    tag = f\"--job-name {method} \"\n",
+    "    resources = f\" --cpus-per-task {par['num_workers']} --mem {par['mem']} --time {par['time']}\" #resources\n",
+    "    tag+=resources\n",
+    "    if method=='scglue':\n",
+    "        tag += f\" --partition=gpu --gres=gpu:1\"\n",
+    "        \n",
+    "    !sbatch {tag} scripts/sbatch/grn_inference.sh \"{command}\" \n",
+    "    # !bash scripts/sbatch/grn_inference.sh \"{command}\" "
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

scripts/sbatch/grn_inference.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+#SBATCH --output=logs/%j.out
+#SBATCH --error=logs/%j.err
+#SBATCH --mail-type=END
+#SBATCH [email protected]
+
+${1}
+# if [ "${1}" = "pearson_corr" ]; then
+#     echo "Method: ${1}"
+#     python src/control_methods/pearson/script.py ${args}
+# elif [ "${1}" = "celloracle" ]; then
+#     /home/jnourisa/miniconda3/envs/celloracle/bin/python src/methods/multi_omics/celloracle/script.py ${args}
+# elif [ "$1" == "scenic" ] || [ "$1" == "genie3" ] || [ "$1" == "grnboost2" ]; then
+#     singularity exec ../../images/scenic python src/methods/single_omics/${1}/script.py ${args}
+# elif [ "$1" == "scglue" ]; then
+#     singularity exec ../../images/${1} python src/methods/multi_omics/${1}/script.py ${args}
+# elif [ "$1" == "ppcor" ]; then #R 
+#     singularity exec ../../images/${1} Rscript src/methods/single_omics/${1}/script.R ${args}
+# else
+#     singularity exec ../../images/${1} python src/methods/single_omics/${1}/script.py ${args}
+# fi
+
+
+
+

src/control_methods/pearson/script.py

@@ -3,13 +3,38 @@
 par = {
     'multiomics_rna': 'resources/grn-benchmark/multiomics_rna_0.h5ad',
     'tf_all': 'resources/prior/tf_all.csv',
-    'cell_type_specific': True,
+    'cell_type_specific': False,
     'max_n_links': 50000,
     'prediction': 'resources/grn_models/donor_0_default/pearson.csv',
     "seed": 32,
     'normalize': False
 }
 ## VIASH END
+meta = {
+    'resources_dir': 'src/utils'
+    }
+
+import argparse
+parser = argparse.ArgumentParser(description="Process multiomics RNA data.")
+parser.add_argument('--multiomics_rna', type=str, help='Path to the multiomics RNA file')
+parser.add_argument('--prediction', type=str, help='Path to the prediction file')
+parser.add_argument('--resources_dir', type=str, help='Path to the prediction file')
+parser.add_argument('--tf_all', type=str, help='Path to the tf_all')
+parser.add_argument('--num_workers', type=str, help='Number of cores')
+args = parser.parse_args()
+
+if args.multiomics_rna:
+    par['multiomics_rna'] = args.multiomics_rna
+if args.prediction:
+    par['prediction'] = args.prediction
+if args.tf_all:
+    par['tf_all'] = args.tf_all
+if args.num_workers:
+    par['num_workers'] = args.num_workers
+
+if args.resources_dir:
+    meta['resources_dir'] = args.resources_dir  
+
 import sys
 sys.path.append(meta["resources_dir"])
 from util import create_corr_net