Update Phosphorylation_experiment_specific_RT_prediction_using_AutoRT…

…_Colab.ipynb
bzhanglab · Oct 12, 2021 · 00ad8e8 · 00ad8e8
1 parent 38693a0
commit 00ad8e8
Showing 1 changed file with 24 additions and 11 deletions.
diff --git a/example/Phosphorylation_experiment_specific_RT_prediction_using_AutoRT_Colab.ipynb b/example/Phosphorylation_experiment_specific_RT_prediction_using_AutoRT_Colab.ipynb
@@ -29,6 +29,7 @@
         "<a href=\"https://colab.research.google.com/github/bzhanglab/AutoRT/blob/master/example/Phosphorylation_experiment_specific_RT_prediction_using_AutoRT_Colab.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
       ]
     },
+
 
     {
       "cell_type": "markdown",
@@ -68,7 +69,7 @@
         "! git clone https://github.com/bzhanglab/AutoRT\n",
         "! ls -l -t"
       ],
-      "execution_count": 1,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "stream",
@@ -138,7 +139,7 @@
         "# check the file in current folder\n",
         "%ls -l"
       ],
-      "execution_count": 3,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "stream",
@@ -177,7 +178,7 @@
         "print(\"The number of rows: %d\" % (evidence_df.shape[0]))\n",
         "evidence_df.head()"
       ],
-      "execution_count": 28,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "stream",
@@ -646,7 +647,7 @@
         "## 0.2: the ratio of split for testing data\n",
         "! Rscript AutoRT/example/scripts/generate_training_testing_data_for_single_shot_ptm.R formated_evidence.txt 0.2 ./"
       ],
-      "execution_count": 5,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "stream",
@@ -720,7 +721,7 @@
         "plt.grid(True)\n",
         "plt.show()\n"
       ],
-      "execution_count": 8,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "display_data",
@@ -778,7 +779,7 @@
       "source": [
         "! python AutoRT/autort.py train -i train_data.tsv -o tf_model/ -e 40 -b 64 -u m -m AutoRT/models/ptm_base_model/phosphorylation_sty/model.json -rlr -n 10"
       ],
-      "execution_count": 9,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "stream",
@@ -2291,7 +2292,7 @@
       "source": [
         "! ls -l tf_model/"
       ],
-      "execution_count": 10,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "stream",
@@ -2370,7 +2371,7 @@
         "test_data = pd.read_csv(\"test_data.tsv\",sep=\"\\t\")\n",
         "test_data.head()"
       ],
-      "execution_count": 11,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "execute_result",
@@ -2495,7 +2496,7 @@
       "source": [
         "! python AutoRT/autort.py predict -t test_data.tsv -s tf_model/model.json -o tf_prediction/ -p test"
       ],
-      "execution_count": 12,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "stream",
@@ -2638,7 +2639,7 @@
       "source": [
         "! ls -l tf_prediction/"
       ],
-      "execution_count": 13,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "stream",
@@ -2661,6 +2662,18 @@
         }
       ]
     },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "ZpCiC1c7D2jd"
+      },
+      "source": [
+        "pred_data = pd.read_csv(\"tf_prediction/test.tsv\",sep=\"\\t\")\n",
+        "pred_data.head()"
+      ],
+      "execution_count": null,
+      "outputs": []
+    },
     {
       "cell_type": "markdown",
       "metadata": {
@@ -2706,7 +2719,7 @@
         "plt.grid(True)\n",
         "plt.show()"
       ],
-      "execution_count": 27,
+      "execution_count": null,
       "outputs": [
         {
           "output_type": "display_data",