update

case_studies/Integrating third-party tools.ipynb

@@ -8,7 +8,10 @@
     "Executing any shell command with pyrpipe is easy and straight-forward. \n",
     "\n",
     "The `Runnable` class can used to import any Unix command into python in an object oriented manner. The `Runnable` class executes all commands via the `pyrpipe_engine` module, which provides helper functions to easily execute and log shell commands. \n",
-    "Users can directly use `execute_command()` function from `pyrpipe_engine` to directly run Unix commands."
+    "Users can directly use `execute_command()` function from `pyrpipe_engine` to directly run Unix commands.\n",
+    "\n",
+    "**NOTE:** Inexperienced users must be careful when executing shell commands as some commands can be dangerous and cause loss of data or even worse. Same applies when executing shell commands via `pyrpipe`. `pyrpipe` provides `--dry-run` option that users can use to see the shell commands without executing them (Use this before running any scripts shared via a source you dont trust (also go through the python code)).  In pyrpipe only the `get_shell_output()` method provides `shell=True` option for subprocess.  This comes in handy when executing commands that relies on environment variables, pipes, output redirection etc., but can also execute commands like `rm -r *` which deletes everything in the current working directory.\n",
+    "`pyrpipe` has a `--safe-mode` flag that can disable `rm` commands.\n"
    ]
   },
   {
@@ -140,27 +143,30 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\u001b[93mStart:21-01-01 13:43:51\u001b[0m\n",
+      "\u001b[93mReading configuration from pyrpipe_conf.yaml\u001b[0m\n",
+      "\u001b[93mStart:21-01-17 19:04:34\u001b[0m\n",
       "\u001b[96m$ ls -l\u001b[0m\n",
       "\u001b[96mSTDOUT:\n",
-      "total 44\n",
-      "drwxr-xr-x 7 usingh usingh  4096 Apr  6  2020 Athaliana_transcript_assembly\n",
-      "drwxr-xr-x 2 usingh usingh  4096 Apr  6  2020 Human_annotation_snakemake\n",
-      "-rw-r--r-- 1 usingh usingh 14373 Jan  1 13:42 Integrating third-party tools.ipynb\n",
-      "drwxr-xr-x 9 usingh usingh  4096 Apr  6  2020 Maize_lncRNA_prediction\n",
-      "drwxr-xr-x 2 usingh usingh  4096 Jan  1 13:43 orfipy_out\n",
-      "-rw-r--r-- 1 usingh usingh    12 Dec 31 17:03 pyrpipe_conf.yaml\n",
-      "drwxr-xr-x 2 usingh usingh  4096 Dec 31 17:02 pyrpipe_logs\n",
-      "drwxr-xr-x 3 usingh usingh  4096 Mar  7  2020 sample_data\n",
+      "total 56\n",
+      "drwxr-xr-x  8 usingh usingh  4096 Jan  4 15:00 Athaliana_transcript_assembly\n",
+      "drwxr-xr-x  4 usingh usingh  4096 Jan 17 13:41 Covid_RNA-Seq\n",
+      "drwxr-xr-x  3 usingh usingh  4096 Jan 11 11:24 GTEx_processing\n",
+      "-rw-r--r--  1 usingh usingh 16955 Jan 17 19:00 Integrating third-party tools.ipynb\n",
+      "drwxr-xr-x 11 usingh usingh  4096 Jan  4 15:00 Maize_lncRNA_prediction\n",
+      "drwxr-xr-x  2 usingh usingh  4096 Jan  4 15:00 orfipy_out\n",
+      "-rw-r--r--  1 usingh usingh    12 Jan  4 15:00 pyrpipe_conf.yaml\n",
+      "drwxr-xr-x  2 usingh usingh  4096 Dec 31 17:02 pyrpipe_logs\n",
+      "drwxr-xr-x  3 usingh usingh  4096 Mar  7  2020 sample_data\n",
+      "drwxr-xr-x  3 usingh usingh  4096 Jan  5 12:24 Snakemake_example\n",
       "\u001b[0m\n",
-      "\u001b[93mEnd:21-01-01 13:43:51\u001b[0m\n",
+      "\u001b[93mEnd:21-01-17 19:04:34\u001b[0m\n",
       "\u001b[92mTime taken:0:00:00\u001b[0m\n"
      ]
     },
@@ -170,7 +176,7 @@
        "True"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 1,
      "metadata": {},
      "output_type": "execute_result"
     }

pyrpipe/__init__.py

@@ -280,8 +280,7 @@ def init_sys_args(self):
 elif sys.argv[0].split('/')[-1]=='pyrpipe':
     #will go to __main__.main
     pass
-else:
-
+else:    
     run_py=False
     _full_command=' '.join(sys.argv)
     #this will execute in command was like python <script.py> [opts]

tests/test_conf.py

@@ -54,17 +54,17 @@ def test_pipeline1():
 
 def test_pipeline2():    
     st=sraOb.trim(tg).align(hs).assemble(stie).quant(kl)   
-    assert st!=None,"pipeline 1 failed"
+    assert st!=None,"pipeline 2 failed"
 
 
 def test_pipeline3():    
     st=sraOb.trim(tg).align(star).assemble(stie).quant(sl)   
-    assert st!=None,"pipeline 1 failed"
+    assert st!=None,"pipeline 3 failed"
 
 
 def test_pipeline4():    
     st=sraOb.quant(sl).quant(kl).align(star)
-    assert st!=None,"pipeline 1 failed"
+    assert st!=None,"pipeline 4 failed"
 
 def test_remove():
     assert pe.delete_file('pyrpipe_conf.yaml')==True,'removing conf.yaml failed'