annotate clsi_profile_type2_linux-Copy1.ipynb @ 1:9c7d056cac30 draft

"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 2d3fa913c9fa9db73f4aa40799749f2247abaa80-dirty"

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "967b1345",
   "metadata": {},
   "outputs": [],
   "source": [
    "# ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics\n",
    "# By [e-mail], 06-Jun-2021\n",
    "import pandas as pd\n",
    "import re\n",
    "import sys"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "39e25c15",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.4 2.2.1\n"
     ]
    }
   ],
   "source": [
    "print(pd.__version__, re.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 175,
   "id": "c96d7c62",
   "metadata": {},
   "outputs": [],
   "source": [
    "# cross check MIC values\n",
    "def sus_res(mic):\n",
    "    print(mic)\n",
    "    #print ((mic,pd.isna(mic[1]),pd.isna(mic[0]),'\\n')\n",
    "    if not (pd.isna(mic[0]) or pd.isna(mic[1]) or pd.isna(mic[2])):#check for NaN value\n",
    "        #remove unwanted whitespace\n",
    "        o_mic = mic[0].replace(' ', '')\n",
    "        s_mic = mic[1].replace(' ', '')\n",
    "        r_mic = mic[2].replace(' ', '')\n",
    "        i_mic = mic[3].replace(' ', '')\n",
    "        print(imic(o_mic,i_mic))\n",
    "        #print (o_mic,s_mic,r_mic)\n",
    "        #print (type(o_mic),type(s_mic),type(r_mic))\n",
    "        if '/' in s_mic: #check for combination antibiotics\n",
    "            #print ('combination antibiotics')\n",
    "            try:\n",
    "                if '/' in o_mic:\n",
    "                    #print ('input combination')\n",
    "                    if (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(o_mic.split('/')[1]) <= float(s_mic.split('/')[1])):\n",
    "                        strain_type='Susceptible'\n",
    "                    elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(o_mic.split('/')[1]) >= float(r_mic.split('/')[1])):\n",
    "                        strain_type='Resistant'\n",
    "                    elif (imic(o_mic,i_mic)):\n",
    "                        strain_type='Intermediate-1'                    \n",
    "                    else:\n",
    "                        strain_type='Intermediate-2'\n",
    "                else: \n",
    "                    #print ('single')\n",
    "                    if float(o_mic)==0:\n",
    "                        strain_type='Strain could not classified'\n",
    "                    elif (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(1) <= float(s_mic.split('/')[1])):\n",
    "                        strain_type='Susceptible'\n",
    "                    elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(1) >= float(r_mic.split('/')[1])):\n",
    "                        strain_type='Resistant'\n",
    "                    else:\n",
    "                        strain_type='Intermediate-3'\n",
    "            except ValueError:\n",
    "                strain_type='Strain could not classified-1'\n",
    "        elif (s_mic == '-'):\n",
    "            if o_mic:\n",
    "                if float(o_mic)==0:\n",
    "                    strain_type='Strain could not classified-2'\n",
    "                #elif (float(o_mic) <= float(s_mic)):\n",
    "                #    strain_type='Susceptible'\n",
    "                elif (float(o_mic) >= float(r_mic)):\n",
    "                    strain_type='Resistant'\n",
    "                elif (imic(o_mic,i_mic)):\n",
    "                    strain_type='Intermediat-4'\n",
    "                else:\n",
    "                    strain_type='Intermediate-5'\n",
    "            else:\n",
    "                strain_type='Strain could not classified-3'\n",
    "        else: #single antibiotics\n",
    "            #print('single antibiotics')\n",
    "            if o_mic:\n",
    "                if float(o_mic)==0:\n",
    "                    strain_type='Strain could not classified-4'\n",
    "                elif (float(o_mic) <= float(s_mic)):\n",
    "                    strain_type='Susceptible'\n",
    "                elif (float(o_mic) >= float(r_mic)):\n",
    "                    strain_type='Resistant'\n",
    "                else:\n",
    "                    strain_type='Intermediate-6'\n",
    "            else:\n",
    "                strain_type='Strain could not classified-5'\n",
    "    else:\n",
    "        strain_type='Strain could not classified-6'\n",
    "    return(strain_type)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 176,
   "id": "dbc70e34",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['32/2', '16/4', '128/4', '32/4-64/4']\n",
      "32/2 32/4-64/4\n",
      "False\n",
      "32/2 32/4-64/4\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'Intermediate-2'"
      ]
     },
     "execution_count": 176,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mic=['32/2','16/4','128/4','32/4-64/4']\n",
    "sus_res(mic)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "653b096e",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 202,
   "id": "626a1e3f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "65/4 64/4 s\n",
      "65 4 64 4 s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'Strain could not classified-5'"
      ]
     },
     "execution_count": 202,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "def check_mic(mic1,mic2,mic_type):\n",
    "    print(mic1,mic2,mic_type)\n",
    "    m1a = mic1.split('/')[0]\n",
    "    m1b = mic1.split('/')[1]\n",
    "    if '-' in mic2:   # for intermediate only\n",
    "        m2a = mic2.split('-')[0].split('/')[0]\n",
    "        m2b = mic2.split('-')[0].split('/')[1]\n",
    "        m2aa = mic2.split('-')[1].split('/')[0]\n",
    "        m2bb = mic2.split('-')[1].split('/')[1]\n",
    "        if (float(m2aa)>=float(m1a)>=float(m2a) and float(m2b)>=float(m1b)>=float(m2b)):\n",
    "            #print('intermediate')\n",
    "            mic_type='Intermediate-1'\n",
    "        else:\n",
    "            #print('not define')\n",
    "            mic_type='Strain could not classified-1'\n",
    "        #print (m1a,m1b,m2a,m2b,m2aa,m2bb)\n",
    "    else:\n",
    "        m2a = mic2.split('/')[0]\n",
    "        m2b = mic2.split('/')[1]\n",
    "        print(m1a,m1b,m2a,m2b,mic_type)\n",
    "        if mic_type=='s':\n",
    "            if (float(m1a)<=float(m2a) and float(m1b)<=float(m2b)):\n",
    "                mic_type='Susceptible'\n",
    "            else:\n",
    "                mic_type='Strain could not classified-5'\n",
    "        elif mic_type=='r':\n",
    "            if (float(m1a)>=float(m2a) and float(m1b)>=float(m2b)):\n",
    "                mic_type='Resistant'\n",
    "            else:\n",
    "                mic_type='Strain could not classified-4'\n",
    "        elif mic_type=='i':\n",
    "            if (float(m1a)==float(m2a) and float(m1b)==float(m2b)):\n",
    "                mic_type='Intermediate-2'\n",
    "            else:\n",
    "                mic_type='Strain could not classified-3'\n",
    "        else:\n",
    "            mic_type='Strain could not classified-2'\n",
    "    return(mic_type)\n",
    "        \n",
    "check_mic('65/4','64/4','s')\n",
    "#    float(mic1.split('/')[0]) <= float(mic2.split('/')[0]) and float(mic1.split('/')[1]) <= float(mic2.split('/')[1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 171,
   "id": "19905924",
   "metadata": {},
   "outputs": [],
   "source": [
    "#compare MIC values and assign Susceptible and Resistant to Strain\n",
    "#try:\n",
    "#result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res,axis = 1)\n",
    "#except ValueError:\n",
    "#    print('Waring: Error in input MIC value')\n",
    "#result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res,axis = 1)\n",
    "#del result['CLSI_profile']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "id": "7784b77d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'input_user = sys.argv[1]\\ninput_clsi = sys.argv[2]\\noutput_table = sys.argv[3]'"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# for input argument\n",
    "\"\"\"input_user = sys.argv[1]\n",
    "input_clsi = sys.argv[2]\n",
    "output_table = sys.argv[3]\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "id": "1dee9127",
   "metadata": {},
   "outputs": [],
   "source": [
    "input_user='input.csv'\n",
    "input_clsi='clsi.csv'\n",
    "output_profile=input_user+'_profile.csv'\n",
    "output_table=input_user+'_table.csv'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "14c5cfd3",
   "metadata": {},
   "outputs": [],
   "source": [
    "# read user AST data with selected 3 columns\n",
    "strain_mic=pd.read_csv(input_user, sep=',', usecols =['Strain name', 'Antibiotics', 'MIC'],na_filter=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "77135cb7",
   "metadata": {},
   "outputs": [],
   "source": [
    "clsi_bp=pd.read_csv(input_clsi,sep=',')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "2ec1cbec",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
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       "    }\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>Antibiotics</th>\n",
       "      <th>Susceptible</th>\n",
       "      <th>Resistant</th>\n",
       "      <th>Intermediate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Amikacin</td>\n",
       "      <td>≤ 16</td>\n",
       "      <td>≥ 64</td>\n",
       "      <td>32</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Tobramycin</td>\n",
       "      <td>≤ 4</td>\n",
       "      <td>≥ 16</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Gentamicin</td>\n",
       "      <td>≤ 4</td>\n",
       "      <td>≥ 16</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Netilmicin</td>\n",
       "      <td>≤ 8</td>\n",
       "      <td>≥ 32</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Imipenem</td>\n",
       "      <td>≤ 2</td>\n",
       "      <td>≥ 8</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Meropenem</td>\n",
       "      <td>≤ 2</td>\n",
       "      <td>≥ 8</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Doripenem</td>\n",
       "      <td>≤ 2</td>\n",
       "      <td>≥ 8</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Ciprofloxacin</td>\n",
       "      <td>≤ 1</td>\n",
       "      <td>≥ 4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Levofloxacin</td>\n",
       "      <td>≤ 2</td>\n",
       "      <td>≥ 8</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Piperacillin/ tazobactam</td>\n",
       "      <td>≤ 16/4</td>\n",
       "      <td>≥ 128/4</td>\n",
       "      <td>32/4-64/4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Ticarcillin/ clavulanic acid</td>\n",
       "      <td>≤ 16/2</td>\n",
       "      <td>≥ 128/2</td>\n",
       "      <td>32/2-64/2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Cefotaxime</td>\n",
       "      <td>≤ 8</td>\n",
       "      <td>≥ 64</td>\n",
       "      <td>16-32</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Ceftriaxone</td>\n",
       "      <td>≤ 8</td>\n",
       "      <td>≥ 64</td>\n",
       "      <td>16-32</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Ceftazidime</td>\n",
       "      <td>≤ 8</td>\n",
       "      <td>≥ 32</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Cefepime</td>\n",
       "      <td>≤ 8</td>\n",
       "      <td>≥ 32</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Trimethoprim/ sulfamethoxazole</td>\n",
       "      <td>≤ 2/38</td>\n",
       "      <td>≥ 4/76</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Ampicillin/ sulbactam</td>\n",
       "      <td>≤ 8/4</td>\n",
       "      <td>≥ 32/16</td>\n",
       "      <td>16/8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Colistin</td>\n",
       "      <td>-</td>\n",
       "      <td>≥ 4</td>\n",
       "      <td>≤ 2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Polymyxin B</td>\n",
       "      <td>-</td>\n",
       "      <td>≥ 4</td>\n",
       "      <td>≤ 2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>Tetracycline</td>\n",
       "      <td>≤ 4</td>\n",
       "      <td>≥ 16</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>Doxycycline</td>\n",
       "      <td>≤ 4</td>\n",
       "      <td>≥ 16</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>Minocycline</td>\n",
       "      <td>≤ 4</td>\n",
       "      <td>≥ 16</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                       Antibiotics Susceptible Resistant Intermediate\n",
       "0                         Amikacin        ≤ 16      ≥ 64           32\n",
       "1                       Tobramycin         ≤ 4      ≥ 16            8\n",
       "2                       Gentamicin         ≤ 4      ≥ 16            8\n",
       "3                       Netilmicin         ≤ 8      ≥ 32           16\n",
       "4                         Imipenem         ≤ 2       ≥ 8            4\n",
       "5                        Meropenem         ≤ 2       ≥ 8            4\n",
       "6                        Doripenem         ≤ 2       ≥ 8            4\n",
       "7                    Ciprofloxacin         ≤ 1       ≥ 4            2\n",
       "8                     Levofloxacin         ≤ 2       ≥ 8            4\n",
       "9         Piperacillin/ tazobactam      ≤ 16/4   ≥ 128/4    32/4-64/4\n",
       "10    Ticarcillin/ clavulanic acid      ≤ 16/2   ≥ 128/2    32/2-64/2\n",
       "11                      Cefotaxime         ≤ 8      ≥ 64        16-32\n",
       "12                     Ceftriaxone         ≤ 8      ≥ 64        16-32\n",
       "13                     Ceftazidime         ≤ 8      ≥ 32           16\n",
       "14                        Cefepime         ≤ 8      ≥ 32           16\n",
       "15  Trimethoprim/ sulfamethoxazole      ≤ 2/38    ≥ 4/76            -\n",
       "16           Ampicillin/ sulbactam       ≤ 8/4   ≥ 32/16         16/8\n",
       "17                        Colistin           -       ≥ 4          ≤ 2\n",
       "18                     Polymyxin B           -       ≥ 4          ≤ 2\n",
       "19                    Tetracycline         ≤ 4      ≥ 16            8\n",
       "20                     Doxycycline         ≤ 4      ≥ 16            8\n",
       "21                     Minocycline         ≤ 4      ≥ 16            8"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "clsi_bp\n",
    "#strain_mic"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "860505f7",
   "metadata": {},
   "outputs": [],
   "source": [
    "# convert MIC to numbers sMIC, rMIC\n",
    "clsi_bp['s_mic'] =clsi_bp[['Susceptible']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n",
    "clsi_bp['r_mic'] =clsi_bp[['Resistant']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n",
    "clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "cad964a6",
   "metadata": {},
   "outputs": [],
   "source": [
    "#clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "2b6c02f5",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Read only numbers in MIC values\n",
    "#try:\n",
    "strain_mic['o_mic']=strain_mic[['MIC']].applymap(lambda x: (re.sub(r'[^0-9.\\/]','', x)))\n",
    "#except TypeError:\n",
    "#    print('Waring: Error in MIC value')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "942fefb2",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</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",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Acinetobacter baumannii A85</td>\n",
       "      <td>Colistin</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Acinetobacter baumannii A85</td>\n",
       "      <td>Colistin</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Acinetobacter baumannii A85</td>\n",
       "      <td>Colistin</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Ampicillin</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Ampicillin/sulbactam</td>\n",
       "      <td>mg/L</td>\n",
       "      <td>/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Piperacillin/tazobactam</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Cefazolin</td>\n",
       "      <td>64</td>\n",
       "      <td>64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Ceftriaxone</td>\n",
       "      <td>16</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Cefepime</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Meropenem</td>\n",
       "      <td>0.25</td>\n",
       "      <td>0.25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Imipenem</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Tigecycline</td>\n",
       "      <td>0.5</td>\n",
       "      <td>0.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
       "      <td>Ceftazidime</td>\n",
       "      <td>&gt;128</td>\n",
       "      <td>128</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
       "      <td>Cefepime</td>\n",
       "      <td>&gt;256</td>\n",
       "      <td>256</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
       "      <td>Ciprofloxacin</td>\n",
       "      <td>&gt;32</td>\n",
       "      <td>32</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Colistin</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Trimethoprim/sulfamethoxazole</td>\n",
       "      <td>8/152</td>\n",
       "      <td>8/152</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Ampicillin/sulbactam</td>\n",
       "      <td>&gt;=0.3 mg/L</td>\n",
       "      <td>0.3/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Ticarcillin/clavulanicacid</td>\n",
       "      <td>&gt;=128/2</td>\n",
       "      <td>128/2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Piperacillin/tazobactam</td>\n",
       "      <td>NA</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Trimethoprim/sulfamethoxazole</td>\n",
       "      <td>8/152</td>\n",
       "      <td>8/152</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>Acinetobacter baumannii ORAB01</td>\n",
       "      <td>Piperacillin/tazobactam</td>\n",
       "      <td>&gt;64/4</td>\n",
       "      <td>64/4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>Acinetobacter baumannii strain MRSN7100</td>\n",
       "      <td>Amoxicillin/clavulanicacid</td>\n",
       "      <td>16/8</td>\n",
       "      <td>16/8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>Acinetobacter baumannii strain MRSN7168</td>\n",
       "      <td>Amoxicillin/clavulanicacid</td>\n",
       "      <td>16/8</td>\n",
       "      <td>16/8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>Acinetobacter baumannii strain MRSN7336</td>\n",
       "      <td>Amoxicillin/clavulanicacid</td>\n",
       "      <td>16/8</td>\n",
       "      <td>16/8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>Acinetobacter baumannii strain MRSN7834</td>\n",
       "      <td>Amoxicillin/clavulanicacid</td>\n",
       "      <td>16/8</td>\n",
       "      <td>16/8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0305</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0306</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0307</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0308</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                       Strain name  \\\n",
       "0                      Acinetobacter baumannii A85   \n",
       "1                      Acinetobacter baumannii A85   \n",
       "2                      Acinetobacter baumannii A85   \n",
       "3               Acinetobacter baumannii AB307-0294   \n",
       "4               Acinetobacter baumannii AB307-0294   \n",
       "5               Acinetobacter baumannii AB307-0294   \n",
       "6               Acinetobacter baumannii AB307-0294   \n",
       "7               Acinetobacter baumannii AB307-0294   \n",
       "8               Acinetobacter baumannii AB307-0294   \n",
       "9               Acinetobacter baumannii AB307-0294   \n",
       "10              Acinetobacter baumannii AB307-0294   \n",
       "11              Acinetobacter baumannii AB307-0294   \n",
       "12               Acinetobacter baumannii AB5075-UW   \n",
       "13               Acinetobacter baumannii AB5075-UW   \n",
       "14               Acinetobacter baumannii AB5075-UW   \n",
       "15                   Acinetobacter baumannii DU202   \n",
       "16                   Acinetobacter baumannii DU202   \n",
       "17                   Acinetobacter baumannii DU202   \n",
       "18                   Acinetobacter baumannii DU202   \n",
       "19                   Acinetobacter baumannii DU202   \n",
       "20                   Acinetobacter baumannii DU202   \n",
       "21                  Acinetobacter baumannii ORAB01   \n",
       "22         Acinetobacter baumannii strain MRSN7100   \n",
       "23         Acinetobacter baumannii strain MRSN7168   \n",
       "24         Acinetobacter baumannii strain MRSN7336   \n",
       "25         Acinetobacter baumannii strain MRSN7834   \n",
       "26  Acinetobacter baumannii strain FDA-CDC-AR_0305   \n",
       "27  Acinetobacter baumannii strain FDA-CDC-AR_0306   \n",
       "28  Acinetobacter baumannii strain FDA-CDC-AR_0307   \n",
       "29  Acinetobacter baumannii strain FDA-CDC-AR_0308   \n",
       "\n",
       "                      Antibiotics         MIC  o_mic  \n",
       "0                        Colistin         0.1    0.1  \n",
       "1                        Colistin           1      1  \n",
       "2                        Colistin           2      2  \n",
       "3                      Ampicillin           0      0  \n",
       "4            Ampicillin/sulbactam        mg/L      /  \n",
       "5         Piperacillin/tazobactam           0      0  \n",
       "6                       Cefazolin          64     64  \n",
       "7                     Ceftriaxone          16     16  \n",
       "8                        Cefepime           8      8  \n",
       "9                       Meropenem        0.25   0.25  \n",
       "10                       Imipenem           1      1  \n",
       "11                    Tigecycline         0.5    0.5  \n",
       "12                    Ceftazidime        >128    128  \n",
       "13                       Cefepime        >256    256  \n",
       "14                  Ciprofloxacin         >32     32  \n",
       "15                       Colistin                     \n",
       "16  Trimethoprim/sulfamethoxazole       8/152  8/152  \n",
       "17           Ampicillin/sulbactam  >=0.3 mg/L   0.3/  \n",
       "18     Ticarcillin/clavulanicacid     >=128/2  128/2  \n",
       "19        Piperacillin/tazobactam          NA         \n",
       "20  Trimethoprim/sulfamethoxazole       8/152  8/152  \n",
       "21        Piperacillin/tazobactam       >64/4   64/4  \n",
       "22     Amoxicillin/clavulanicacid        16/8   16/8  \n",
       "23     Amoxicillin/clavulanicacid        16/8   16/8  \n",
       "24     Amoxicillin/clavulanicacid        16/8   16/8  \n",
       "25     Amoxicillin/clavulanicacid        16/8   16/8  \n",
       "26                     Polymyxinb           1      1  \n",
       "27                     Polymyxinb           1      1  \n",
       "28                     Polymyxinb           8      8  \n",
       "29                     Polymyxinb           4      4  "
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "strain_mic"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "bba6b0a2",
   "metadata": {},
   "outputs": [],
   "source": [
    "# capitalize each Antibiotic Name for comparision with removing whitespace\n",
    "strain_mic['Antibiotics']=strain_mic['Antibiotics'].str.capitalize().str.replace(\" \",\"\")\n",
    "clsi_bp['Antibiotics']=clsi_bp['Antibiotics'].str.capitalize().str.replace(\" \",\"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "id": "ea403928",
   "metadata": {},
   "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",
       "      <th>s_mic</th>\n",
       "      <th>r_mic</th>\n",
       "      <th>i_mic</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Acinetobacter baumannii A85</td>\n",
       "      <td>Colistin</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Acinetobacter baumannii A85</td>\n",
       "      <td>Colistin</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Acinetobacter baumannii A85</td>\n",
       "      <td>Colistin</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Colistin</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Ampicillin/sulbactam</td>\n",
       "      <td>mg/L</td>\n",
       "      <td>/</td>\n",
       "      <td>8/4</td>\n",
       "      <td>32/16</td>\n",
       "      <td>16/8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Ampicillin/sulbactam</td>\n",
       "      <td>&gt;=0.3 mg/L</td>\n",
       "      <td>0.3/</td>\n",
       "      <td>8/4</td>\n",
       "      <td>32/16</td>\n",
       "      <td>16/8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Piperacillin/tazobactam</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>16/4</td>\n",
       "      <td>128/4</td>\n",
       "      <td>32/4-64/4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Piperacillin/tazobactam</td>\n",
       "      <td>NA</td>\n",
       "      <td></td>\n",
       "      <td>16/4</td>\n",
       "      <td>128/4</td>\n",
       "      <td>32/4-64/4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Acinetobacter baumannii ORAB01</td>\n",
       "      <td>Piperacillin/tazobactam</td>\n",
       "      <td>&gt;64/4</td>\n",
       "      <td>64/4</td>\n",
       "      <td>16/4</td>\n",
       "      <td>128/4</td>\n",
       "      <td>32/4-64/4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Ceftriaxone</td>\n",
       "      <td>16</td>\n",
       "      <td>16</td>\n",
       "      <td>8</td>\n",
       "      <td>64</td>\n",
       "      <td>16-32</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Cefepime</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>32</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
       "      <td>Cefepime</td>\n",
       "      <td>&gt;256</td>\n",
       "      <td>256</td>\n",
       "      <td>8</td>\n",
       "      <td>32</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Meropenem</td>\n",
       "      <td>0.25</td>\n",
       "      <td>0.25</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Imipenem</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
       "      <td>Ceftazidime</td>\n",
       "      <td>&gt;128</td>\n",
       "      <td>128</td>\n",
       "      <td>8</td>\n",
       "      <td>32</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
       "      <td>Ciprofloxacin</td>\n",
       "      <td>&gt;32</td>\n",
       "      <td>32</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Trimethoprim/sulfamethoxazole</td>\n",
       "      <td>8/152</td>\n",
       "      <td>8/152</td>\n",
       "      <td>2/38</td>\n",
       "      <td>4/76</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Trimethoprim/sulfamethoxazole</td>\n",
       "      <td>8/152</td>\n",
       "      <td>8/152</td>\n",
       "      <td>2/38</td>\n",
       "      <td>4/76</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Ticarcillin/clavulanicacid</td>\n",
       "      <td>&gt;=128/2</td>\n",
       "      <td>128/2</td>\n",
       "      <td>16/2</td>\n",
       "      <td>128/2</td>\n",
       "      <td>32/2-64/2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0305</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0306</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0307</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0308</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                       Strain name  \\\n",
       "0                      Acinetobacter baumannii A85   \n",
       "1                      Acinetobacter baumannii A85   \n",
       "2                      Acinetobacter baumannii A85   \n",
       "3                    Acinetobacter baumannii DU202   \n",
       "4               Acinetobacter baumannii AB307-0294   \n",
       "5                    Acinetobacter baumannii DU202   \n",
       "6               Acinetobacter baumannii AB307-0294   \n",
       "7                    Acinetobacter baumannii DU202   \n",
       "8                   Acinetobacter baumannii ORAB01   \n",
       "9               Acinetobacter baumannii AB307-0294   \n",
       "10              Acinetobacter baumannii AB307-0294   \n",
       "11               Acinetobacter baumannii AB5075-UW   \n",
       "12              Acinetobacter baumannii AB307-0294   \n",
       "13              Acinetobacter baumannii AB307-0294   \n",
       "14               Acinetobacter baumannii AB5075-UW   \n",
       "15               Acinetobacter baumannii AB5075-UW   \n",
       "16                   Acinetobacter baumannii DU202   \n",
       "17                   Acinetobacter baumannii DU202   \n",
       "18                   Acinetobacter baumannii DU202   \n",
       "19  Acinetobacter baumannii strain FDA-CDC-AR_0305   \n",
       "20  Acinetobacter baumannii strain FDA-CDC-AR_0306   \n",
       "21  Acinetobacter baumannii strain FDA-CDC-AR_0307   \n",
       "22  Acinetobacter baumannii strain FDA-CDC-AR_0308   \n",
       "\n",
       "                      Antibiotics         MIC  o_mic s_mic  r_mic      i_mic  \n",
       "0                        Colistin         0.1    0.1     -      4          2  \n",
       "1                        Colistin           1      1     -      4          2  \n",
       "2                        Colistin           2      2     -      4          2  \n",
       "3                        Colistin                        -      4          2  \n",
       "4            Ampicillin/sulbactam        mg/L      /   8/4  32/16       16/8  \n",
       "5            Ampicillin/sulbactam  >=0.3 mg/L   0.3/   8/4  32/16       16/8  \n",
       "6         Piperacillin/tazobactam           0      0  16/4  128/4  32/4-64/4  \n",
       "7         Piperacillin/tazobactam          NA         16/4  128/4  32/4-64/4  \n",
       "8         Piperacillin/tazobactam       >64/4   64/4  16/4  128/4  32/4-64/4  \n",
       "9                     Ceftriaxone          16     16     8     64      16-32  \n",
       "10                       Cefepime           8      8     8     32         16  \n",
       "11                       Cefepime        >256    256     8     32         16  \n",
       "12                      Meropenem        0.25   0.25     2      8          4  \n",
       "13                       Imipenem           1      1     2      8          4  \n",
       "14                    Ceftazidime        >128    128     8     32         16  \n",
       "15                  Ciprofloxacin         >32     32     1      4          2  \n",
       "16  Trimethoprim/sulfamethoxazole       8/152  8/152  2/38   4/76          -  \n",
       "17  Trimethoprim/sulfamethoxazole       8/152  8/152  2/38   4/76          -  \n",
       "18     Ticarcillin/clavulanicacid     >=128/2  128/2  16/2  128/2  32/2-64/2  \n",
       "19                     Polymyxinb           1      1     -      4          2  \n",
       "20                     Polymyxinb           1      1     -      4          2  \n",
       "21                     Polymyxinb           8      8     -      4          2  \n",
       "22                     Polymyxinb           4      4     -      4          2  "
      ]
     },
     "execution_count": 53,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#compare CLSI Antibiotics only\n",
    "#result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner',  indicator=True)[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','_merge']]\n",
    "try:\n",
    "    result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner')[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','i_mic']]\n",
    "except KeyError:\n",
    "    print('Waring: Error in input Values')\n",
    "result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "id": "44f7e35d",
   "metadata": {},
   "outputs": [
    {
     "ename": "ValueError",
     "evalue": "could not broadcast input array from shape (23,) into shape (23,1)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-44-76a7d8475ba3>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m#compare MIC values and assign Susceptible and Resistant to Strain\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0;31m#try:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mresult\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'CLSI_profile'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'o_mic'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m's_mic'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m'r_mic'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m'i_mic'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msus_res\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0maxis\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[0m\u001b[1;32m      4\u001b[0m \u001b[0;31m#except ValueError:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;31m#    print('Waring: Error in input MIC value')\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36m__setitem__\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m   3158\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_frame\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3159\u001b[0m         \u001b[0;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mSeries\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndarray\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mIndex\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3160\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_array\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   3161\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3162\u001b[0m             \u001b[0;31m# set column\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36m_setitem_array\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m   3196\u001b[0m                 )[1]\n\u001b[1;32m   3197\u001b[0m                 \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_check_setitem_copy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3198\u001b[0;31m                 \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0miloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   3199\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3200\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_setitem_frame\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m__setitem__\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m    690\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    691\u001b[0m         \u001b[0miloc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"iloc\"\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0miloc\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 692\u001b[0;31m         \u001b[0miloc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_with_indexer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    693\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    694\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_validate_key\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m_setitem_with_indexer\u001b[0;34m(self, indexer, value, name)\u001b[0m\n\u001b[1;32m   1635\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_with_indexer_split_path\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1636\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1637\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_single_block\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1638\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1639\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_setitem_with_indexer_split_path\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m_setitem_single_block\u001b[0;34m(self, indexer, value, name)\u001b[0m\n\u001b[1;32m   1859\u001b[0m         \u001b[0;31m# actually do the set\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1860\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_consolidate_inplace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1861\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_mgr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_mgr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetitem\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1862\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_maybe_update_cacher\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mclear\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1863\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/internals/managers.py\u001b[0m in \u001b[0;36msetitem\u001b[0;34m(self, indexer, value)\u001b[0m\n\u001b[1;32m    566\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    567\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0msetitem\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;34m\"BlockManager\"\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 568\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"setitem\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    569\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    570\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mputmask\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmask\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnew\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0malign\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mbool\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/internals/managers.py\u001b[0m in \u001b[0;36mapply\u001b[0;34m(self, f, align_keys, ignore_failures, **kwargs)\u001b[0m\n\u001b[1;32m    425\u001b[0m                     \u001b[0mapplied\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    426\u001b[0m                 \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 427\u001b[0;31m                     \u001b[0mapplied\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mb\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    428\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mTypeError\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mNotImplementedError\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    429\u001b[0m                 \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mignore_failures\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/internals/blocks.py\u001b[0m in \u001b[0;36msetitem\u001b[0;34m(self, indexer, value)\u001b[0m\n\u001b[1;32m   1033\u001b[0m         \u001b[0;31m# set\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1034\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1035\u001b[0;31m             \u001b[0mvalues\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1036\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1037\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mtranspose\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mValueError\u001b[0m: could not broadcast input array from shape (23,) into shape (23,1)"
     ]
    }
   ],
   "source": [
    "#compare MIC values and assign Susceptible and Resistant to Strain\n",
    "#try:\n",
    "result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res,axis = 1)\n",
    "#except ValueError:\n",
    "#    print('Waring: Error in input MIC value')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "id": "30c2a7a3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\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",
       "      <th>s_mic</th>\n",
       "      <th>r_mic</th>\n",
       "      <th>i_mic</th>\n",
       "      <th>CLSI_profile</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Acinetobacter baumannii A85</td>\n",
       "      <td>Colistin</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.1</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>Intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Acinetobacter baumannii A85</td>\n",
       "      <td>Colistin</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>Intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Acinetobacter baumannii A85</td>\n",
       "      <td>Colistin</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>IntermediatE</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Colistin</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>Strain could not classified</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Ampicillin/sulbactam</td>\n",
       "      <td>mg/L</td>\n",
       "      <td>/</td>\n",
       "      <td>8/4</td>\n",
       "      <td>32/16</td>\n",
       "      <td>16/8</td>\n",
       "      <td>Strain could not classified</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Ampicillin/sulbactam</td>\n",
       "      <td>&gt;=0.3 mg/L</td>\n",
       "      <td>0.3/</td>\n",
       "      <td>8/4</td>\n",
       "      <td>32/16</td>\n",
       "      <td>16/8</td>\n",
       "      <td>Strain could not classified</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Piperacillin/tazobactam</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>16/4</td>\n",
       "      <td>128/4</td>\n",
       "      <td>32/4-64/4</td>\n",
       "      <td>Strain could not classified</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Piperacillin/tazobactam</td>\n",
       "      <td>NA</td>\n",
       "      <td></td>\n",
       "      <td>16/4</td>\n",
       "      <td>128/4</td>\n",
       "      <td>32/4-64/4</td>\n",
       "      <td>Strain could not classified</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Acinetobacter baumannii ORAB01</td>\n",
       "      <td>Piperacillin/tazobactam</td>\n",
       "      <td>&gt;64/4</td>\n",
       "      <td>64/4</td>\n",
       "      <td>16/4</td>\n",
       "      <td>128/4</td>\n",
       "      <td>32/4-64/4</td>\n",
       "      <td>Intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Ceftriaxone</td>\n",
       "      <td>16</td>\n",
       "      <td>16</td>\n",
       "      <td>8</td>\n",
       "      <td>64</td>\n",
       "      <td>16-32</td>\n",
       "      <td>Intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Cefepime</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>32</td>\n",
       "      <td>16</td>\n",
       "      <td>Susceptible</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
       "      <td>Cefepime</td>\n",
       "      <td>&gt;256</td>\n",
       "      <td>256</td>\n",
       "      <td>8</td>\n",
       "      <td>32</td>\n",
       "      <td>16</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Meropenem</td>\n",
       "      <td>0.25</td>\n",
       "      <td>0.25</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "      <td>4</td>\n",
       "      <td>Susceptible</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
       "      <td>Imipenem</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "      <td>4</td>\n",
       "      <td>Susceptible</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
       "      <td>Ceftazidime</td>\n",
       "      <td>&gt;128</td>\n",
       "      <td>128</td>\n",
       "      <td>8</td>\n",
       "      <td>32</td>\n",
       "      <td>16</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
       "      <td>Ciprofloxacin</td>\n",
       "      <td>&gt;32</td>\n",
       "      <td>32</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Trimethoprim/sulfamethoxazole</td>\n",
       "      <td>8/152</td>\n",
       "      <td>8/152</td>\n",
       "      <td>2/38</td>\n",
       "      <td>4/76</td>\n",
       "      <td>-</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Trimethoprim/sulfamethoxazole</td>\n",
       "      <td>8/152</td>\n",
       "      <td>8/152</td>\n",
       "      <td>2/38</td>\n",
       "      <td>4/76</td>\n",
       "      <td>-</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Acinetobacter baumannii DU202</td>\n",
       "      <td>Ticarcillin/clavulanicacid</td>\n",
       "      <td>&gt;=128/2</td>\n",
       "      <td>128/2</td>\n",
       "      <td>16/2</td>\n",
       "      <td>128/2</td>\n",
       "      <td>32/2-64/2</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0305</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>Intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0306</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>Intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0307</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0308</td>\n",
       "      <td>Polymyxinb</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>-</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                       Strain name  \\\n",
       "0                      Acinetobacter baumannii A85   \n",
       "1                      Acinetobacter baumannii A85   \n",
       "2                      Acinetobacter baumannii A85   \n",
       "3                    Acinetobacter baumannii DU202   \n",
       "4               Acinetobacter baumannii AB307-0294   \n",
       "5                    Acinetobacter baumannii DU202   \n",
       "6               Acinetobacter baumannii AB307-0294   \n",
       "7                    Acinetobacter baumannii DU202   \n",
       "8                   Acinetobacter baumannii ORAB01   \n",
       "9               Acinetobacter baumannii AB307-0294   \n",
       "10              Acinetobacter baumannii AB307-0294   \n",
       "11               Acinetobacter baumannii AB5075-UW   \n",
       "12              Acinetobacter baumannii AB307-0294   \n",
       "13              Acinetobacter baumannii AB307-0294   \n",
       "14               Acinetobacter baumannii AB5075-UW   \n",
       "15               Acinetobacter baumannii AB5075-UW   \n",
       "16                   Acinetobacter baumannii DU202   \n",
       "17                   Acinetobacter baumannii DU202   \n",
       "18                   Acinetobacter baumannii DU202   \n",
       "19  Acinetobacter baumannii strain FDA-CDC-AR_0305   \n",
       "20  Acinetobacter baumannii strain FDA-CDC-AR_0306   \n",
       "21  Acinetobacter baumannii strain FDA-CDC-AR_0307   \n",
       "22  Acinetobacter baumannii strain FDA-CDC-AR_0308   \n",
       "\n",
       "                      Antibiotics         MIC  o_mic s_mic  r_mic      i_mic  \\\n",
       "0                        Colistin         0.1    0.1     -      4          2   \n",
       "1                        Colistin           1      1     -      4          2   \n",
       "2                        Colistin           2      2     -      4          2   \n",
       "3                        Colistin                        -      4          2   \n",
       "4            Ampicillin/sulbactam        mg/L      /   8/4  32/16       16/8   \n",
       "5            Ampicillin/sulbactam  >=0.3 mg/L   0.3/   8/4  32/16       16/8   \n",
       "6         Piperacillin/tazobactam           0      0  16/4  128/4  32/4-64/4   \n",
       "7         Piperacillin/tazobactam          NA         16/4  128/4  32/4-64/4   \n",
       "8         Piperacillin/tazobactam       >64/4   64/4  16/4  128/4  32/4-64/4   \n",
       "9                     Ceftriaxone          16     16     8     64      16-32   \n",
       "10                       Cefepime           8      8     8     32         16   \n",
       "11                       Cefepime        >256    256     8     32         16   \n",
       "12                      Meropenem        0.25   0.25     2      8          4   \n",
       "13                       Imipenem           1      1     2      8          4   \n",
       "14                    Ceftazidime        >128    128     8     32         16   \n",
       "15                  Ciprofloxacin         >32     32     1      4          2   \n",
       "16  Trimethoprim/sulfamethoxazole       8/152  8/152  2/38   4/76          -   \n",
       "17  Trimethoprim/sulfamethoxazole       8/152  8/152  2/38   4/76          -   \n",
       "18     Ticarcillin/clavulanicacid     >=128/2  128/2  16/2  128/2  32/2-64/2   \n",
       "19                     Polymyxinb           1      1     -      4          2   \n",
       "20                     Polymyxinb           1      1     -      4          2   \n",
       "21                     Polymyxinb           8      8     -      4          2   \n",
       "22                     Polymyxinb           4      4     -      4          2   \n",
       "\n",
       "                   CLSI_profile  \n",
       "0                  Intermediate  \n",
       "1                  Intermediate  \n",
       "2                  IntermediatE  \n",
       "3   Strain could not classified  \n",
       "4   Strain could not classified  \n",
       "5   Strain could not classified  \n",
       "6   Strain could not classified  \n",
       "7   Strain could not classified  \n",
       "8                  Intermediate  \n",
       "9                  Intermediate  \n",
       "10                  Susceptible  \n",
       "11                    Resistant  \n",
       "12                  Susceptible  \n",
       "13                  Susceptible  \n",
       "14                    Resistant  \n",
       "15                    Resistant  \n",
       "16                    Resistant  \n",
       "17                    Resistant  \n",
       "18                    Resistant  \n",
       "19                 Intermediate  \n",
       "20                 Intermediate  \n",
       "21                    Resistant  \n",
       "22                    Resistant  "
      ]
     },
     "execution_count": 61,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "ab7d8379",
   "metadata": {},
   "outputs": [],
   "source": [
    "#result[['Strain name', 'Antibiotics', 'MIC','s_mic','r_mic','CLSI_profile']].to_csv(output_profile,sep=',', index=False, encoding='utf-8-sig')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "a426ae2b",
   "metadata": {},
   "outputs": [],
   "source": [
    "#create a pivot table for ASIST\n",
    "table=result[['Strain name', 'Antibiotics','CLSI_profile']].drop_duplicates()\n",
    "result_table=pd.pivot_table(table, values ='CLSI_profile', index =['Strain name'],columns =['Antibiotics'], aggfunc = lambda x: ' '.join(x))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "df439a58",
   "metadata": {},
   "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>Antibiotics</th>\n",
       "      <th>Ampicillin/sulbactam</th>\n",
       "      <th>Cefepime</th>\n",
       "      <th>Ceftazidime</th>\n",
       "      <th>Ceftriaxone</th>\n",
       "      <th>Ciprofloxacin</th>\n",
       "      <th>Colistin</th>\n",
       "      <th>Imipenem</th>\n",
       "      <th>Meropenem</th>\n",
       "      <th>Piperacillin/tazobactam</th>\n",
       "      <th>Polymyxinb</th>\n",
       "      <th>Ticarcillin/clavulanicacid</th>\n",
       "      <th>Trimethoprim/sulfamethoxazole</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Strain name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii A85</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii AB307-0294</th>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Intermediate</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii AB5075-UW</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii DU202</th>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii ORAB01</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Intermediate</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii strain FDA-CDC-AR_0305</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii strain FDA-CDC-AR_0306</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii strain FDA-CDC-AR_0307</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii strain FDA-CDC-AR_0308</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Antibiotics                                            Ampicillin/sulbactam  \\\n",
       "Strain name                                                                   \n",
       "Acinetobacter baumannii A85                                             NaN   \n",
       "Acinetobacter baumannii AB307-0294              Strain could not classified   \n",
       "Acinetobacter baumannii AB5075-UW                                       NaN   \n",
       "Acinetobacter baumannii DU202                   Strain could not classified   \n",
       "Acinetobacter baumannii ORAB01                                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                          NaN   \n",
       "\n",
       "Antibiotics                                        Cefepime Ceftazidime  \\\n",
       "Strain name                                                               \n",
       "Acinetobacter baumannii A85                             NaN         NaN   \n",
       "Acinetobacter baumannii AB307-0294              Susceptible         NaN   \n",
       "Acinetobacter baumannii AB5075-UW                 Resistant   Resistant   \n",
       "Acinetobacter baumannii DU202                           NaN         NaN   \n",
       "Acinetobacter baumannii ORAB01                          NaN         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305          NaN         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306          NaN         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307          NaN         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308          NaN         NaN   \n",
       "\n",
       "Antibiotics                                      Ceftriaxone Ciprofloxacin  \\\n",
       "Strain name                                                                  \n",
       "Acinetobacter baumannii A85                              NaN           NaN   \n",
       "Acinetobacter baumannii AB307-0294              Intermediate           NaN   \n",
       "Acinetobacter baumannii AB5075-UW                        NaN     Resistant   \n",
       "Acinetobacter baumannii DU202                            NaN           NaN   \n",
       "Acinetobacter baumannii ORAB01                           NaN           NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305           NaN           NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306           NaN           NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307           NaN           NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308           NaN           NaN   \n",
       "\n",
       "Antibiotics                                                        Colistin  \\\n",
       "Strain name                                                                   \n",
       "Acinetobacter baumannii A85                                     Susceptible   \n",
       "Acinetobacter baumannii AB307-0294                                      NaN   \n",
       "Acinetobacter baumannii AB5075-UW                                       NaN   \n",
       "Acinetobacter baumannii DU202                   Strain could not classified   \n",
       "Acinetobacter baumannii ORAB01                                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                          NaN   \n",
       "\n",
       "Antibiotics                                        Imipenem    Meropenem  \\\n",
       "Strain name                                                                \n",
       "Acinetobacter baumannii A85                             NaN          NaN   \n",
       "Acinetobacter baumannii AB307-0294              Susceptible  Susceptible   \n",
       "Acinetobacter baumannii AB5075-UW                       NaN          NaN   \n",
       "Acinetobacter baumannii DU202                           NaN          NaN   \n",
       "Acinetobacter baumannii ORAB01                          NaN          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305          NaN          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306          NaN          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307          NaN          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308          NaN          NaN   \n",
       "\n",
       "Antibiotics                                         Piperacillin/tazobactam  \\\n",
       "Strain name                                                                   \n",
       "Acinetobacter baumannii A85                                             NaN   \n",
       "Acinetobacter baumannii AB307-0294              Strain could not classified   \n",
       "Acinetobacter baumannii AB5075-UW                                       NaN   \n",
       "Acinetobacter baumannii DU202                   Strain could not classified   \n",
       "Acinetobacter baumannii ORAB01                                 Intermediate   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                          NaN   \n",
       "\n",
       "Antibiotics                                      Polymyxinb  \\\n",
       "Strain name                                                   \n",
       "Acinetobacter baumannii A85                             NaN   \n",
       "Acinetobacter baumannii AB307-0294                      NaN   \n",
       "Acinetobacter baumannii AB5075-UW                       NaN   \n",
       "Acinetobacter baumannii DU202                           NaN   \n",
       "Acinetobacter baumannii ORAB01                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305  Susceptible   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306  Susceptible   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307    Resistant   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308    Resistant   \n",
       "\n",
       "Antibiotics                                    Ticarcillin/clavulanicacid  \\\n",
       "Strain name                                                                 \n",
       "Acinetobacter baumannii A85                                           NaN   \n",
       "Acinetobacter baumannii AB307-0294                                    NaN   \n",
       "Acinetobacter baumannii AB5075-UW                                     NaN   \n",
       "Acinetobacter baumannii DU202                                   Resistant   \n",
       "Acinetobacter baumannii ORAB01                                        NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                        NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                        NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                        NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                        NaN   \n",
       "\n",
       "Antibiotics                                    Trimethoprim/sulfamethoxazole  \n",
       "Strain name                                                                   \n",
       "Acinetobacter baumannii A85                                              NaN  \n",
       "Acinetobacter baumannii AB307-0294                                       NaN  \n",
       "Acinetobacter baumannii AB5075-UW                                        NaN  \n",
       "Acinetobacter baumannii DU202                                      Resistant  \n",
       "Acinetobacter baumannii ORAB01                                           NaN  \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                           NaN  \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                           NaN  \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                           NaN  \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                           NaN  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "result_table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "ee19e872",
   "metadata": {},
   "outputs": [],
   "source": [
    "#result_table.to_csv(output_table,na_rep='NA')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "692ab948",
   "metadata": {},
   "outputs": [],
   "source": [
    "# reorder the Antibiotics for ASIST\n",
    "clsi_ab=['Amikacin','Tobramycin','Gentamycin','Imipenem','Meropenem','Doripenem','Ciprofloxacin','Levofloxacin',\n",
    "         'Piperacillin/tazobactam','Ticarcillin/clavulanicacid','Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime',\n",
    "         'Trimethoprim/sulfamethoxazole','Ampicillin/sulbactam','Colistin','Polymyxinb','Tetracycline','Doxicycline ',\n",
    "         'Minocycline']\n",
    "result_selected=result_table.filter(clsi_ab)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "e0d983b9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(9, 12)"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "result_selected.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "04376d0a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(9, 12)"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "result_table.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "1b0a4d77",
   "metadata": {},
   "outputs": [],
   "source": [
    "result_selected.insert(0,'Resistance_phenotype','')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "d36dcdab",
   "metadata": {},
   "outputs": [],
   "source": [
    "result_selected.to_csv(output_table,na_rep='NA')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "5c162c07",
   "metadata": {},
   "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>Antibiotics</th>\n",
       "      <th>Resistance_phenotype</th>\n",
       "      <th>Imipenem</th>\n",
       "      <th>Meropenem</th>\n",
       "      <th>Ciprofloxacin</th>\n",
       "      <th>Piperacillin/ tazobactam</th>\n",
       "      <th>Ticarcillin/clavulanic acid</th>\n",
       "      <th>Ceftriaxone</th>\n",
       "      <th>Ceftazidime</th>\n",
       "      <th>Cefepime</th>\n",
       "      <th>Trimethoprim/ sulfamethoxazole</th>\n",
       "      <th>Ampicillin/ sulbactam</th>\n",
       "      <th>Colistin</th>\n",
       "      <th>Polymyxin B</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Strain name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii A85</th>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii AB307-0294</th>\n",
       "      <td></td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Intermediate</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Susceptible</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii AB5075-UW</th>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii DU202</th>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>Strain could not classified</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii ORAB01</th>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Intermediate</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii strain FDA-CDC-AR_0305</th>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Susceptible</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii strain FDA-CDC-AR_0306</th>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Susceptible</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii strain FDA-CDC-AR_0307</th>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acinetobacter baumannii strain FDA-CDC-AR_0308</th>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Resistant</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Antibiotics                                    Resistance_phenotype  \\\n",
       "Strain name                                                           \n",
       "Acinetobacter baumannii A85                                           \n",
       "Acinetobacter baumannii AB307-0294                                    \n",
       "Acinetobacter baumannii AB5075-UW                                     \n",
       "Acinetobacter baumannii DU202                                         \n",
       "Acinetobacter baumannii ORAB01                                        \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                        \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                        \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                        \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                        \n",
       "\n",
       "Antibiotics                                        Imipenem    Meropenem  \\\n",
       "Strain name                                                                \n",
       "Acinetobacter baumannii A85                             NaN          NaN   \n",
       "Acinetobacter baumannii AB307-0294              Susceptible  Susceptible   \n",
       "Acinetobacter baumannii AB5075-UW                       NaN          NaN   \n",
       "Acinetobacter baumannii DU202                           NaN          NaN   \n",
       "Acinetobacter baumannii ORAB01                          NaN          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305          NaN          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306          NaN          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307          NaN          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308          NaN          NaN   \n",
       "\n",
       "Antibiotics                                    Ciprofloxacin  \\\n",
       "Strain name                                                    \n",
       "Acinetobacter baumannii A85                              NaN   \n",
       "Acinetobacter baumannii AB307-0294                       NaN   \n",
       "Acinetobacter baumannii AB5075-UW                  Resistant   \n",
       "Acinetobacter baumannii DU202                            NaN   \n",
       "Acinetobacter baumannii ORAB01                           NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305           NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306           NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307           NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308           NaN   \n",
       "\n",
       "Antibiotics                                        Piperacillin/ tazobactam  \\\n",
       "Strain name                                                                   \n",
       "Acinetobacter baumannii A85                                             NaN   \n",
       "Acinetobacter baumannii AB307-0294              Strain could not classified   \n",
       "Acinetobacter baumannii AB5075-UW                                       NaN   \n",
       "Acinetobacter baumannii DU202                   Strain could not classified   \n",
       "Acinetobacter baumannii ORAB01                                 Intermediate   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                          NaN   \n",
       "\n",
       "Antibiotics                                    Ticarcillin/clavulanic acid  \\\n",
       "Strain name                                                                  \n",
       "Acinetobacter baumannii A85                                            NaN   \n",
       "Acinetobacter baumannii AB307-0294                                     NaN   \n",
       "Acinetobacter baumannii AB5075-UW                                      NaN   \n",
       "Acinetobacter baumannii DU202                                    Resistant   \n",
       "Acinetobacter baumannii ORAB01                                         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                         NaN   \n",
       "\n",
       "Antibiotics                                      Ceftriaxone Ceftazidime  \\\n",
       "Strain name                                                                \n",
       "Acinetobacter baumannii A85                              NaN         NaN   \n",
       "Acinetobacter baumannii AB307-0294              Intermediate         NaN   \n",
       "Acinetobacter baumannii AB5075-UW                        NaN   Resistant   \n",
       "Acinetobacter baumannii DU202                            NaN         NaN   \n",
       "Acinetobacter baumannii ORAB01                           NaN         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305           NaN         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306           NaN         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307           NaN         NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308           NaN         NaN   \n",
       "\n",
       "Antibiotics                                        Cefepime  \\\n",
       "Strain name                                                   \n",
       "Acinetobacter baumannii A85                             NaN   \n",
       "Acinetobacter baumannii AB307-0294              Susceptible   \n",
       "Acinetobacter baumannii AB5075-UW                 Resistant   \n",
       "Acinetobacter baumannii DU202                           NaN   \n",
       "Acinetobacter baumannii ORAB01                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308          NaN   \n",
       "\n",
       "Antibiotics                                    Trimethoprim/ sulfamethoxazole  \\\n",
       "Strain name                                                                     \n",
       "Acinetobacter baumannii A85                                               NaN   \n",
       "Acinetobacter baumannii AB307-0294                                        NaN   \n",
       "Acinetobacter baumannii AB5075-UW                                         NaN   \n",
       "Acinetobacter baumannii DU202                                       Resistant   \n",
       "Acinetobacter baumannii ORAB01                                            NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                            NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                            NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                            NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                            NaN   \n",
       "\n",
       "Antibiotics                                           Ampicillin/ sulbactam  \\\n",
       "Strain name                                                                   \n",
       "Acinetobacter baumannii A85                                             NaN   \n",
       "Acinetobacter baumannii AB307-0294              Strain could not classified   \n",
       "Acinetobacter baumannii AB5075-UW                                       NaN   \n",
       "Acinetobacter baumannii DU202                   Strain could not classified   \n",
       "Acinetobacter baumannii ORAB01                                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                          NaN   \n",
       "\n",
       "Antibiotics                                                        Colistin  \\\n",
       "Strain name                                                                   \n",
       "Acinetobacter baumannii A85                                     Susceptible   \n",
       "Acinetobacter baumannii AB307-0294                                      NaN   \n",
       "Acinetobacter baumannii AB5075-UW                                       NaN   \n",
       "Acinetobacter baumannii DU202                   Strain could not classified   \n",
       "Acinetobacter baumannii ORAB01                                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307                          NaN   \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308                          NaN   \n",
       "\n",
       "Antibiotics                                     Polymyxin B  \n",
       "Strain name                                                  \n",
       "Acinetobacter baumannii A85                             NaN  \n",
       "Acinetobacter baumannii AB307-0294                      NaN  \n",
       "Acinetobacter baumannii AB5075-UW                       NaN  \n",
       "Acinetobacter baumannii DU202                           NaN  \n",
       "Acinetobacter baumannii ORAB01                          NaN  \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0305  Susceptible  \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0306  Susceptible  \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0307    Resistant  \n",
       "Acinetobacter baumannii strain FDA-CDC-AR_0308    Resistant  "
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#rename headers\n",
    "result_selected.rename(columns = {'Ticarcillin/clavulanicacid':'Ticarcillin/clavulanic acid','Piperacillin/tazobactam':'Piperacillin/ tazobactam','Trimethoprim/sulfamethoxazole': 'Trimethoprim/ sulfamethoxazole','Ampicillin/sulbactam':'Ampicillin/ sulbactam', 'Polymyxinb': 'Polymyxin B'} )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "00cd53d4",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "475401df",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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