Documented how to suppress GODag output messages.

#155 #133
tanghaibao · Feb 22, 2020 · 1baa3b7 · 1baa3b7
1 parent 357f359
commit 1baa3b7
Showing 1 changed file with 30 additions and 13 deletions.
diff --git a/notebooks/godag_obsolete_terms.ipynb b/notebooks/godag_obsolete_terms.ipynb
@@ -41,7 +41,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -67,7 +67,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -82,6 +82,23 @@
     "godag = GODag(fin_dag, optional_attrs={'consider', 'replaced_by'}, load_obsolete=True)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 3a) How to suppress the GODag output messages\n",
+    "Set argument: `prt=None`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "godag = GODag(fin_dag, optional_attrs={'consider', 'replaced_by'}, load_obsolete=True, prt=None)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -91,19 +108,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "2,717 GO terms are obsolete\n",
-      "1 GO:0006158 was replaced by GO:0046936\n",
-      "2 GO:0006197 was replaced by GO:0003876\n",
-      "3 GO:0006155 was replaced by GO:0004000\n",
-      "4 GO:0030601 was replaced by GO:0004177\n",
-      "5 GO:0030602 was replaced by GO:0004190\n"
+      "1 GO:0030303 was replaced by GO:0004222\n",
+      "2 GO:0046560 was replaced by GO:0004190\n",
+      "3 GO:0046561 was replaced by GO:0004190\n",
+      "4 GO:0046908 was replaced by GO:0050801\n",
+      "5 GO:0030271 was replaced by GO:0004252\n"
      ]
     }
    ],
@@ -137,11 +154,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "1 Given GO:0003801, consider {'GO:0004252', 'GO:0007596'}\n",
-      "2 Given GO:0006162, consider {'GO:0004748'}\n",
-      "3 Given GO:0004005, consider {'GO:0019829', 'GO:0005886'}\n",
-      "4 Given GO:0010320, consider {'GO:0004197', 'GO:0004175'}\n",
-      "5 Given GO:0008539, consider {'GO:0004866', 'GO:0061136'}\n"
+      "1 Given GO:0016658, consider {'GO:0042602', 'GO:0008752'}\n",
+      "2 Given GO:0016583, consider {'GO:0006334'}\n",
+      "3 Given GO:0016585, consider {'GO:0006338'}\n",
+      "4 Given GO:0046909, consider {'GO:0016192', 'GO:0120009'}\n",
+      "5 Given GO:0045012, consider {'GO:0032395', 'GO:0042613'}\n"
      ]
     }
    ],