create metadata utils and exe file

Author: fefossa

metadata/Get_metadata_from_csv_layout.ipynb

@@ -114,15 +114,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 53,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "C:\\Users\\Fer\\Documents\\GitHub\\2022_09_09_LiveCellPainting_fossa_Cimini\\analysis\\2022_06_07_DILI\\2023_new_batch\\metadata\\layout_day2.xlsx\n",
-      "layout_day2\n"
+      "C:\\Users\\Fer\\Documents\\GitHub\\2022_09_09_LiveCellPainting_fossa_Cimini\\metadata\\layout\\2023_new_batch_DILI\\layout_day1.xlsx\n",
+      "layout_day1\n"
      ]
     }
    ],
@@ -142,7 +142,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 54,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -152,14 +152,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 55,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "['None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'Huh7 Aspirin 10 trt', 'Huh7 Aspirin 10 trt', 'Huh7 Aspirin 10 trt', 'Huh7 Aspirin 10 trt', 'Huh7 Aspirin 1 trt', 'Huh7 Aspirin 1 trt', 'Huh7 Aspirin 1 trt', 'Huh7 Aspirin 1 trt', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'None', 'None', 'Huh7 Cyclophosphamide 10 trt', 'Huh7 Cyclophosphamide 10 trt', 'Huh7 Cyclophosphamide 10 trt', 'Huh7 Cyclophosphamide 10 trt', 'Huh7 Cyclophosphamide 1 trt', 'Huh7 Cyclophosphamide 1 trt', 'Huh7 Cyclophosphamide 1 trt', 'Huh7 Cyclophosphamide 1 trt', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'None', 'None', 'Huh7 Orphenadrine 10 trt', 'Huh7 Orphenadrine 10 trt', 'Huh7 Orphenadrine 10 trt', 'Huh7 Orphenadrine 10 trt', 'Huh7 Orphenadrine 1 trt', 'Huh7 Orphenadrine 1 trt', 'Huh7 Orphenadrine 1 trt', 'Huh7 Orphenadrine 1 trt', 'Huh7 Lovastatin 1 trt', 'Huh7 Lovastatin 10 trt', 'None', 'None', 'Huh7 Amiodarone 10 trt', 'Huh7 Amiodarone 10 trt', 'Huh7 Amiodarone 10 trt', 'Huh7 Amiodarone 10 trt', 'Huh7 Amiodarone 1 trt', 'Huh7 Amiodarone 1 trt', 'Huh7 Amiodarone 1 trt', 'Huh7 Amiodarone 1 trt', 'Huh7 Lovastatin 1 trt', 'Huh7 Lovastatin 10 trt', 'None', 'None', 'Huh7 Lactose 10 negcon', 'Huh7 Lactose 10 negcon', 'Huh7 Lactose 10 negcon', 'Huh7 Lactose 10 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Lovastatin 1 trt', 'Huh7 Lovastatin 10 trt', 'None', 'None', 'Huh7 Etoposide 10 trt', 'Huh7 Etoposide 10 trt', 'Huh7 Etoposide 10 trt', 'Huh7 Etoposide 10 trt', 'Huh7 Etoposide 1 trt', 'Huh7 Etoposide 1 trt', 'Huh7 Etoposide 1 trt', 'Huh7 Etoposide 1 trt', 'Huh7 Lovastatin 1 trt', 'Huh7 Lovastatin 10 trt', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None']\n"
+      "['None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'Huh7 Amiodarone 1 trt', 'Huh7 Amiodarone 1 trt', 'Huh7 Amiodarone 1 trt', 'Huh7 Amiodarone 1 trt', 'Huh7 Amiodarone 10 trt', 'Huh7 Amiodarone 10 trt', 'Huh7 Amiodarone 10 trt', 'Huh7 Amiodarone 10 trt', 'Huh7 Cyclophosphamide 1 trt', 'Huh7 Cyclophosphamide 10 trt', 'None', 'None', 'Huh7 Lovastatin 1 trt', 'Huh7 Lovastatin 1 trt', 'Huh7 Lovastatin 1 trt', 'Huh7 Lovastatin 1 trt', 'Huh7 Lovastatin 10 trt', 'Huh7 Lovastatin 10 trt', 'Huh7 Lovastatin 10 trt', 'Huh7 Lovastatin 10 trt', 'Huh7 Cyclophosphamide 1 trt', 'Huh7 Cyclophosphamide 10 trt', 'None', 'None', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Non-treated 0 negcon', 'Huh7 Cyclophosphamide 1 trt', 'Huh7 Cyclophosphamide 10 trt', 'None', 'None', 'Huh7 Etoposide 1 trt', 'Huh7 Etoposide 1 trt', 'Huh7 Etoposide 1 trt', 'Huh7 Etoposide 1 trt', 'Huh7 Etoposide 10 trt', 'Huh7 Etoposide 10 trt', 'Huh7 Etoposide 10 trt', 'Huh7 Etoposide 10 trt', 'Huh7 Cyclophosphamide 1 trt', 'Huh7 Cyclophosphamide 10 trt', 'None', 'None', 'Huh7 Orphenadrine 1 trt', 'Huh7 Orphenadrine 1 trt', 'Huh7 Orphenadrine 1 trt', 'Huh7 Orphenadrine 1 trt', 'Huh7 Orphenadrine 10 trt', 'Huh7 Orphenadrine 10 trt', 'Huh7 Orphenadrine 10 trt', 'Huh7 Orphenadrine 10 trt', 'Huh7 Lactose 10 negcon', 'Huh7 Lactose 10 negcon', 'None', 'None', 'Huh7 Aspirin 1 trt', 'Huh7 Aspirin 1 trt', 'Huh7 Aspirin 1 trt', 'Huh7 Aspirin 1 trt', 'Huh7 Aspirin 10 trt', 'Huh7 Aspirin 10 trt', 'Huh7 Aspirin 10 trt', 'Huh7 Aspirin 10 trt', 'Huh7 Lactose 10 negcon', 'Huh7 Lactose 10 negcon', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None', 'None']\n"
      ]
     }
    ],
@@ -176,16 +176,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 56,
+   "execution_count": 29,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['Huh7', 'Amiodarone', '1', 'trt']\n"
+     ]
+    }
+   ],
    "source": [
-    "metadata_cols = [\"well_position\", \"cell_type\", \"compound\", \"concentration_uM\", \"control_type\"]"
+    "# metadata_cols = [\"well_position\", \"cell_type\", \"compound\", \"concentration_uM\", \"control_type\"]\n",
+    "metadata_cols = metadata_utils.get_example_to_name_metadata_cols(samples)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 57,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -203,13 +212,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 58,
+   "execution_count": 33,
    "metadata": {},
    "outputs": [],
    "source": [
-    "platemap_column_title = \"plate_map_name\"\n",
-    "\n",
-    "metadata_cols.insert(0, platemap_column_title)\n",
+    "metadata_cols.insert(0, \"plate_map_name\")\n",
     "sublist_add_platemap = [[file_name] + sublist for sublist in sublist]"
    ]
   },