diff clsi_profile_type2_linux.ipynb @ 5:3c27e5c2a8e9 draft

"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"

--- a/clsi_profile_type2_linux.ipynb	Tue Jun 29 12:15:06 2021 +0000
+++ b/clsi_profile_type2_linux.ipynb	Tue Jun 29 12:58:49 2021 +0000
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 115,
+   "execution_count": 7,
    "id": "9aa0a6f7",
    "metadata": {},
    "outputs": [],
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 116,
+   "execution_count": 8,
    "id": "9af8387e",
    "metadata": {},
    "outputs": [],
@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 117,
+   "execution_count": 9,
    "id": "73d0783c",
    "metadata": {},
    "outputs": [],
@@ -118,7 +118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 118,
+   "execution_count": 10,
    "id": "4d2ab1b1",
    "metadata": {},
    "outputs": [],
@@ -149,19 +149,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 119,
+   "execution_count": 11,
    "id": "0e22ef0d",
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "'# for input argument\\ninput_user = sys.argv[1]\\ninput_clsi = sys.argv[2]\\noutput_table = sys.argv[3]'"
-      ]
-     },
-     "execution_count": 119,
-     "metadata": {},
-     "output_type": "execute_result"
+     "ename": "IndexError",
+     "evalue": "list index out of range",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mIndexError\u001b[0m                                Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-11-26f141926f14>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0minput_user\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0margv\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0minput_clsi\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0margv\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0moutput_table\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0margv\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m3\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mIndexError\u001b[0m: list index out of range"
+     ]
     }
    ],
    "source": [
@@ -173,33 +174,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 49,
    "id": "21d5fe63",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "\"#input_user='~/Jupyterlab_notebook/ASIST_module/strain_profiles_16k.csv.csv'\\ninput_user='test-data/input2.csv'\\ninput_clsi='test-data/clsi.csv'\\noutput_profile='test-data/input2_profile.csv'\\noutput_table='test-data/input2_table.csv'\\n#output_table='/home/rakesh/Jupyterlab_notebook/ASIST_module/strain_profiles_16k_table.csv'\""
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "\"\"\"#input_user='~/Jupyterlab_notebook/ASIST_module/strain_profiles_16k.csv.csv'\n",
-    "input_user='test-data/input2.csv'\n",
+    "\"\"\"input_user='~/Jupyterlab_notebook/ASIST_module/strain_profiles_16k.csv.csv'\n",
+    "#input_user='test-data/input2.csv'\n",
     "input_clsi='test-data/clsi.csv'\n",
     "output_profile='test-data/input2_profile.csv'\n",
-    "output_table='test-data/input2_table.csv'\n",
-    "#output_table='/home/rakesh/Jupyterlab_notebook/ASIST_module/strain_profiles_16k_table.csv'\"\"\""
+    "#output_table='test-data/input2_table.csv'\n",
+    "output_table='/home/rakesh/Jupyterlab_notebook/ASIST_module/strain_profiles_16k_table.csv'\"\"\""
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 146,
+   "execution_count": 60,
    "id": "1e64b025",
    "metadata": {},
    "outputs": [],
@@ -211,7 +201,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 147,
+   "execution_count": 61,
    "id": "0d30ddc3",
    "metadata": {},
    "outputs": [],
@@ -223,7 +213,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 148,
+   "execution_count": 62,
    "id": "a818676d",
    "metadata": {},
    "outputs": [],
@@ -234,27 +224,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 149,
+   "execution_count": 64,
    "id": "c2aae757",
    "metadata": {},
    "outputs": [],
    "source": [
+    "# warn user for duplicate files\n",
     "input_dups=strain_mic[strain_mic[['Strain name','Antibiotics']].duplicated()]\n",
     "if (input_dups.shape[0] == 0):\n",
     "    #print( \"No duplicates\")\n",
     "    pass\n",
     "else:\n",
-    "    input_dups.to_csv(output_table,na_rep='NA')\n",
-    "    with open(output_table, \"a\") as file_object:\n",
+    "    with open(output_table, \"w\") as file_object:\n",
     "    # Append 'hello' at the end of file\n",
-    "        file_object.write('Input File Error: Please remove duplicate/mutiple MIC values for same combination of Strain name and Antibiotics from input file')\n",
-    "    exit()\n",
-    "#input_dups.head()"
+    "        file_object.write('S.No.,Strain name,Antibiotics,MIC\\nInput File Error: Please remove duplicate/mutiple MIC values for same combination of Strain name and Antibiotics from input file\\n')\n",
+    "    input_dups.to_csv(output_table,na_rep='NA', mode='a')\n",
+    "    exit()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 125,
+   "execution_count": 17,
    "id": "c6b4c59b",
    "metadata": {},
    "outputs": [],
@@ -267,7 +257,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 126,
+   "execution_count": 18,
    "id": "d0171f94",
    "metadata": {},
    "outputs": [],
@@ -277,7 +267,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 127,
+   "execution_count": 19,
    "id": "fe45b2dd",
    "metadata": {},
    "outputs": [],
@@ -291,7 +281,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 128,
+   "execution_count": 20,
    "id": "ddbbe4d9",
    "metadata": {},
    "outputs": [],
@@ -301,7 +291,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 129,
+   "execution_count": 21,
    "id": "640508f1",
    "metadata": {},
    "outputs": [],
@@ -315,7 +305,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 130,
+   "execution_count": 22,
    "id": "b87426f4",
    "metadata": {},
    "outputs": [],
@@ -336,12 +326,55 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 131,
+   "execution_count": 23,
    "id": "91bfc94d",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Strain name</th>\n",
+       "      <th>Antibiotics</th>\n",
+       "      <th>MIC</th>\n",
+       "      <th>o_mic</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "Empty DataFrame\n",
+       "Columns: [Strain name, Antibiotics, MIC, o_mic]\n",
+       "Index: []"
+      ]
+     },
+     "execution_count": 23,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "#result"
+    "dups.head()"
    ]
   },
   {