Mercurial > repos > rakesh4osdd > asist
diff clsi_profile_type2_linux-Copy1.ipynb @ 0:c1a77856070c draft
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
| author | rakesh4osdd |
|---|---|
| date | Sat, 26 Jun 2021 07:27:53 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clsi_profile_type2_linux-Copy1.ipynb Sat Jun 26 07:27:53 2021 +0000 @@ -0,0 +1,2461 @@ +{ + "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 rakesh4osdd@gmail.com, 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", + "<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>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": { + "text/html": [ + "<div>\n", + "<style scoped>\n", + " .dataframe tbody tr th:only-of-type {\n", + " vertical-align: middle;\n", + " }\n", + "\n", + " .dataframe tbody tr th {\n", + " vertical-align: top;\n", + " }\n", + "\n", + " .dataframe thead th {\n", + " text-align: right;\n", + " }\n", + "</style>\n", + "<table border=\"1\" class=\"dataframe\">\n", + " <thead>\n", + " <tr style=\"text-align: right;\">\n", + " <th></th>\n", + " <th>Strain name</th>\n", + " <th>Antibiotics</th>\n", + " <th>MIC</th>\n", + " <th>o_mic</th>\n", + " </tr>\n", + " </thead>\n", + " <tbody>\n", + " <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>>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>>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>>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>>=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>>=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>>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>>=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>>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>>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>>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>>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>>=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 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\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", + " }\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", + " <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>>=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>>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>>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>>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>>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>>=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": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.1" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}