Mercurial > repos > rakesh4osdd > asist
view 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 |
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{ "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 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 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\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 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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 }