update example

urmi-21 · Apr 27, 2020 · 73aab61 · 73aab61
1 parent 2e3a027
commit 73aab61
Showing 1 changed file with 23 additions and 13 deletions.
diff --git a/case_studies/Integrating third-party tools.ipynb b/case_studies/Integrating third-party tools.ipynb
@@ -10,23 +10,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[93mLogs will be saved to 2020-03-16-15_33_08_pyrpipe.log\u001b[0m\n",
+      "\u001b[93mLogs will be saved to 2020-04-27-17_20_37_pyrpipe.log\u001b[0m\n",
       "\u001b[94m$ ls -l\u001b[0m\n",
       "\u001b[94mSTDOUT:\n",
       "total 32\n",
-      "drwxr-xr-x 7 usingh usingh 4096 Mar 16 15:19 Athaliana_transcript_assembly\n",
-      "drwxr-xr-x 2 usingh usingh 4096 Mar  7 16:33 Human_annotation_snakemake\n",
-      "-rw-r--r-- 1 usingh usingh 9786 Mar  7 16:33 Integrating third-party tools.ipynb\n",
-      "drwxr-xr-x 9 usingh usingh 4096 Mar 16 15:32 Maize_lncRNA_prediction\n",
-      "drwxr-xr-x 2 usingh usingh 4096 Mar 16 15:33 pyrpipe_logs\n",
-      "drwxr-xr-x 3 usingh usingh 4096 Mar  7 16:33 sample_data\n",
+      "drwxr-xr-x 4 usingh usingh  4096 Mar 21 00:45 Athaliana_transcript_assembly\n",
+      "drwxr-xr-x 2 usingh usingh  4096 Mar 21 00:45 Human_annotation_snakemake\n",
+      "-rw-r--r-- 1 usingh usingh 10952 Apr 27 17:20 Integrating third-party tools.ipynb\n",
+      "drwxr-xr-x 6 usingh usingh  4096 Mar 23 13:16 Maize_lncRNA_prediction\n",
+      "drwxr-xr-x 2 usingh usingh  4096 Apr 27 17:20 pyrpipe_logs\n",
+      "drwxr-xr-x 3 usingh usingh  4096 Feb 27 12:16 sample_data\n",
       "\u001b[0m\n",
       "\u001b[92mTime taken:0:00:00\u001b[0m\n"
      ]
@@ -37,7 +37,7 @@
        "True"
       ]
      },
-     "execution_count": 1,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -224,19 +224,29 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "(0, b'364K\\tsample_data/blast_out2\\n', None)\n"
+      "(0, b'364K\\tsample_data/blast_out2\\n', None)\n",
+      "364K\tsample_data/blast_out2\n",
+      "\n"
      ]
     }
    ],
    "source": [
-    "print(pe.getShellOutput(['du', '-sh','sample_data/blast_out2']))"
+    "result=pe.getShellOutput(['du', '-sh','sample_data/blast_out2'])\n",
+    "#result contains return code, stdout, stderr\n",
+    "print(result)\n",
+    "\n",
+    "#check if command was successful\n",
+    "if result[0] == 0:\n",
+    "    #get the stdout as string\n",
+    "    print(result[1].decode(\"utf-8\"))\n",
+    "    "
    ]
   },
   {
@@ -308,7 +318,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.5"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,