alpine run-ready

WayScience · Jul 11, 2023 · d80adda · d80adda
1 parent 6a3eca1
commit d80adda
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Showing 5 changed files with 15 additions and 15 deletions.
diff --git a/Plate_2_data/4.processing_features/0.merge_sc_plate2.ipynb b/Plate_2_data/4.processing_features/0.merge_sc_plate2.ipynb
@@ -58,7 +58,7 @@
    "source": [
     "# set directory for sqlite files\n",
     "sqlite_dir = pathlib.Path(\n",
-    "    \"/scratch/alpine/[email protected]/sqlite_files\"\n",
+    "    \"/projects/[email protected]/\"\n",
     ").resolve(strict=True)\n",
     "\n",
     "# dictionary with info for the sqlite file from each run\n",

diff --git a/Plate_2_data/4.processing_features/2.combine_sc_runs_plate2.ipynb b/Plate_2_data/4.processing_features/2.combine_sc_runs_plate2.ipynb
@@ -60,13 +60,13 @@
    "outputs": [],
    "source": [
     "# set paths to each individual run file after annotation\n",
-    "first_run_sc_path = pathlib.Path(f\"{annotated_dir}/PBMC_batch_1.parquet\")\n",
-    "second_run_sc_path = pathlib.Path(f\"{annotated_dir}/PBMC_batch_2.parquet\")\n",
-    "third_run_sc_path = pathlib.Path(f\"{annotated_dir}/PBMC_batch_3.parquet\")\n",
-    "fourth_run_sc_path = pathlib.Path(f\"{annotated_dir}/PBMC_batch_4.parquet\")\n",
-    "fifth_run_sc_path = pathlib.Path(f\"{annotated_dir}/PBMC_batch_5.parquet\")\n",
-    "sixth_run_sc_path = pathlib.Path(f\"{annotated_dir}/PBMC_batch_6.parquet\")\n",
-    "seventh_run_sc_path = pathlib.Path(f\"{annotated_dir}/PBMC_batch_7.parquet\")"
+    "first_run_sc_path = pathlib.Path(f\"{annotated_dir}/batch_1_sc.parquet\")\n",
+    "second_run_sc_path = pathlib.Path(f\"{annotated_dir}/batch_2_sc.parquet\")\n",
+    "third_run_sc_path = pathlib.Path(f\"{annotated_dir}/batch_3_sc.parquet\")\n",
+    "fourth_run_sc_path = pathlib.Path(f\"{annotated_dir}/batch_4_sc.parquet\")\n",
+    "fifth_run_sc_path = pathlib.Path(f\"{annotated_dir}/batch_5_sc.parquet\")\n",
+    "sixth_run_sc_path = pathlib.Path(f\"{annotated_dir}/batch_6_sc.parquet\")\n",
+    "seventh_run_sc_path = pathlib.Path(f\"{annotated_dir}/batch_7_sc.parquet\")"
    ]
   },
   {

diff --git a/Plate_2_data/4.processing_features/4.feature_select_sc_plate2.ipynb b/Plate_2_data/4.processing_features/4.feature_select_sc_plate2.ipynb
@@ -46,17 +46,17 @@
    "outputs": [],
    "source": [
     "# directory where normalized parquet file is located\n",
-    "data_dir = pathlib.Path(\"./data/\")\n",
+    "data_dir = pathlib.Path(\"./data/normalized_data\")\n",
     "\n",
     "# directory where the feature selected parquet file is saved to\n",
     "output_dir = pathlib.Path(\"./data/feature_selected_data\")\n",
     "output_dir.mkdir(exist_ok=True)\n",
     "\n",
     "# define input path\n",
-    "normalized_file_path = str(pathlib.Path(f\"{data_dir}/SHSY5Y_sc_norm.parquet\"))\n",
+    "normalized_file_path = str(pathlib.Path(f\"{data_dir}/PBMC_sc_norm.parquet\"))\n",
     "\n",
     "# define ouput path\n",
-    "feature_select_output_file = str(pathlib.Path(f\"{output_dir}/SHSY5Y_sc_norm_fs.parquet\"))"
+    "feature_select_output_file = str(pathlib.Path(f\"{output_dir}/PBMC_sc_norm_fs.parquet\"))"
    ]
   },
   {

diff --git a/Plate_2_data/4.processing_features/5.extract_image_features.ipynb b/Plate_2_data/4.processing_features/5.extract_image_features.ipynb
@@ -63,7 +63,7 @@
     "\n",
     "# set directory for sqlite files\n",
     "sqlite_dir = pathlib.Path(\n",
-    "    \"/scratch/alpine/[email protected]/sqlite_files\"\n",
+    "    \"/projects/[email protected]/\"\n",
     ").resolve(strict=True)\n",
     "\n",
     "# dictionary with info for the sqlite file from each run\n",

diff --git a/Plate_2_data/4.processing_features/processing_features_plate2.sh b/Plate_2_data/4.processing_features/processing_features_plate2.sh
@@ -4,10 +4,10 @@
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 
-#SBATCH --mem=500G
+#SBATCH --mem=600G
 #SBATCH --partition=amem
 #SBATCH --qos=mem
-#SBATCH --time=25:00:00
+#SBATCH --time=48:00:00
 #SBATCH --output=sample-%j.out
 
 module purge
@@ -34,5 +34,5 @@ python scripts/3.normalize_sc_plate2.py
 echo "Feature selecting plate 2 data"
 python scripts/4.feature_select_sc_plate2.py
 echo "Extracting image features from plate 2 data"
-python scripts/5.extract_image_features
+python scripts/5.extract_image_features.py
 echo "Processing of plate 2 data complete"