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run_apobec.ipynb

@@ -1,8 +1,15 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### this cell is to run apobec from the current folder "
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {
     "scrolled": false
    },
@@ -13,15 +20,15 @@
      "text": [
       "\n",
       "               ---------------\n",
-      "               job started at 2019-01-23 18:38:54 ...\n",
+      "               job started at 2022-02-18 11:08:37 ...\n",
       "               ---------------\n",
       "               \n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b30187715d5342088cb296a1c7e270ab",
+       "model_id": "aa7eced278fb488f82bb6734eba3fd22",
        "version_major": 2,
        "version_minor": 0
       },
@@ -36,15 +43,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "exception detected. see log for more details\n",
       "\n",
       "    \n",
-      "    file processed: 3\n",
-      "    time taken: 0.0 hours 1.0 minutes 43 seconds\n",
+      "    file processed: 2\n",
+      "    time taken: 0.0 hours 1.0 minutes 33 seconds\n",
       "    \n",
       "    the results are in the folder 'output_apobec'\n",
       "    \n",
       "    ---------------\n",
-      "    ... job finished at 2019-01-23 18:40:37\n",
+      "    ... job finished at 2022-02-18 11:10:10\n",
       "    ---------------\n",
       "    \n",
       "    \n"
@@ -55,72 +63,30 @@
     "%run ./apobec/count_snp_duplex.py"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### to run from the installation use: "
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "               ---------------\n",
-      "               job started at 2019-01-23 18:40:37 ...\n",
-      "               ---------------\n",
-      "               \n",
-      "collecting snp...\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "9a4e7ddece674734ac2bd0e4919d327e",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "IntProgress(value=0, bar_style='success', max=3)"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "snp collected...\n",
-      "plot consctructed...\n",
-      "spreadsheet saved...\n",
-      "\n",
-      "    \n",
-      "    file processed: 3\n",
-      "    time taken: 0.0 hours 0.0 minutes 3 seconds\n",
-      "    \n",
-      "    the results are in the folder 'output_apobec'\n",
-      "    \n",
-      "    note: difference in the output files names \n",
-      "    is denoted by the time when script finished its work.\n",
-      "    \n",
-      "    ---------------\n",
-      "    ... job finished at 2019-01-23 18:40:41\n",
-      "    ---------------\n",
-      "    \n",
-      "    \n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "%run ./apobec/snp_rate.py"
+    "import apobec"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "%run -m apobec.count_snp_duplex"
+   ]
   }
  ],
  "metadata": {
@@ -139,7 +105,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,