Mercurial > repos > rakesh4osdd > asist
diff clsi_profile_type2_linux.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.ipynb Sat Jun 26 07:27:53 2021 +0000 @@ -0,0 +1,1040 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 37, + "id": "9aa0a6f7", + "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": 38, + "id": "9af8387e", + "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": 39, + "id": "73d0783c", + "metadata": {}, + "outputs": [], + "source": [ + "# compare two MIC value strings\n", + "def check_mic(mic1,mic2,mic_type):\n", + " #print(mic1,mic2,mic_type)\n", + " try:\n", + " if '/' in mic1:\n", + " m1a = mic1.split('/')[0]\n", + " m1b = mic1.split('/')[1]\n", + " if float(m1a)==0 or float(m1b)==0:\n", + " strain_type='Strain could not be classified'\n", + " return(strain_type) \n", + " elif '/' in mic2:\n", + " m1a = mic1\n", + " if float(m1a)==0:\n", + " strain_type='Strain could not be classified'\n", + " return(strain_type) \n", + " m1b = '1'\n", + " elif float(mic1)==0:\n", + " strain_type='Strain could not be classified'\n", + " return(strain_type)\n", + " else:\n", + " m1a = mic1\n", + " \n", + " if '-' in mic2:\n", + " m2a = mic2.split('-')[0]\n", + " m2b = mic2.split('-')[1] \n", + " \n", + " except ValueError:\n", + " strain_type='Strain could not be classified' \n", + " return(strain_type)\n", + " try:\n", + " if '-' in mic2 and mic_type == 'i': # for intermediate only\n", + " if '/' in mic2:\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(m2bb)>=float(m1b)>=float(m2b)):\n", + " #print('intermediate')\n", + " m_type='Intermediate'\n", + " else:\n", + " #print('not define')\n", + " m_type='Strain could not be classified'\n", + " else:\n", + " m2a = mic2.split('-')[0]\n", + " m2b = mic2.split('-')[1] \n", + " if (float(m2b)>=float(m1a)>=float(m2a)):\n", + " #print('intermediate')\n", + " m_type='Intermediate'\n", + " else:\n", + " #print('not define')\n", + " m_type='Strain could not be classified' \n", + " #print (m1a,m1b,m2a,m2b,m2aa,m2bb)\n", + " elif '/' in mic2:\n", + " m2a = mic2.split('/')[0]\n", + " m2b = mic2.split('/')[1]\n", + " #print(m1a,m1b,m2a,m2b,mic_type)\n", + " if (mic_type=='s' and (float(m1a)<=float(m2a) and float(m1b)<=float(m2b))):\n", + " m_type='Susceptible'\n", + " elif (mic_type=='r' and (float(m1a)>=float(m2a) and float(m1b)>=float(m2b))):\n", + " m_type='Resistant'\n", + " elif (mic_type=='i' and (float(m1a)==float(m2a) and float(m1b)==float(m2b))):\n", + " m_type='Intermediate'\n", + " else:\n", + " m_type='Strain could not be classified'\n", + " elif '-' in mic2:\n", + " m_type='Strain could not be classified'\n", + " else:\n", + " m2a=mic2\n", + " if (mic_type=='s' and (float(m1a)<=float(m2a))):\n", + " m_type='Susceptible'\n", + " elif (mic_type=='r' and (float(m1a)>=float(m2a))):\n", + " m_type='Resistant'\n", + " elif (mic_type=='i' and (float(m1a)==float(m2a))):\n", + " m_type='Intermediate'\n", + " else:\n", + " m_type='Strain could not be classified-1' \n", + " except IndexError:\n", + " strain_type='Strain could not be classified-2' \n", + " return(strain_type)\n", + " \n", + " return(m_type)\n", + "\n", + "#check_mic('65','32-64','i')" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "id": "4d2ab1b1", + "metadata": {}, + "outputs": [], + "source": [ + "# compare MIC value in pandas list\n", + "def sus_res_int(mic):\n", + " #print(mic)\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", + " try:\n", + " if check_mic(o_mic,s_mic,'s')=='Susceptible':\n", + " strain_type='Susceptible'\n", + " elif check_mic(o_mic,r_mic,'r')=='Resistant':\n", + " strain_type='Resistant'\n", + " elif check_mic(o_mic,i_mic,'i')=='Intermediate':\n", + " strain_type='Intermediate' \n", + " else:\n", + " strain_type='Strain could not be classified'\n", + " except ValueError:\n", + " strain_type='Strain could not be classified' \n", + " return(strain_type)\n", + "\n", + "#mic=['128','16/4','128/4','32/4-64/4']\n", + "#sus_res_int(mic)" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "id": "0e22ef0d", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'# for input argument\\ninput_user = sys.argv[1]\\ninput_clsi = sys.argv[2]\\noutput_table = sys.argv[3]'" + ] + }, + "execution_count": 41, + "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": 42, + "id": "21d5fe63", + "metadata": {}, + "outputs": [], + "source": [ + "'''input_user='input2.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": 43, + "id": "1e64b025", + "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", + " </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", + " </tr>\n", + " <tr>\n", + " <th>1</th>\n", + " <td>Acinetobacter baumannii A85</td>\n", + " <td>Netilmicin</td>\n", + " <td>1</td>\n", + " </tr>\n", + " <tr>\n", + " <th>2</th>\n", + " <td>Acinetobacter baumannii AB307-0294</td>\n", + " <td>Ampicillin</td>\n", + " <td>0</td>\n", + " </tr>\n", + " <tr>\n", + " <th>3</th>\n", + " <td>Acinetobacter baumannii AB307-0294</td>\n", + " <td>Ampicillin/sulbactam</td>\n", + " <td>mg/L</td>\n", + " </tr>\n", + " <tr>\n", + " <th>4</th>\n", + " <td>Acinetobacter baumannii AB307-0294</td>\n", + " <td>piperacillin/tazobactam</td>\n", + " <td>0</td>\n", + " </tr>\n", + " <tr>\n", + " <th>5</th>\n", + " <td>Acinetobacter baumannii AB307-0294</td>\n", + " <td>Cefazolin</td>\n", + " <td>64</td>\n", + " </tr>\n", + " <tr>\n", + " <th>6</th>\n", + " <td>Acinetobacter baumannii AB307-0294</td>\n", + " <td>Ceftriaxone</td>\n", + " <td>16</td>\n", + " </tr>\n", + " <tr>\n", + " <th>7</th>\n", + " <td>Acinetobacter baumannii AB307-0294</td>\n", + " <td>Cefepime</td>\n", + " <td>8</td>\n", + " </tr>\n", + " <tr>\n", + " <th>8</th>\n", + " <td>Acinetobacter baumannii AB307-0294</td>\n", + " <td>Meropenem</td>\n", + " <td>0.25</td>\n", + " </tr>\n", + " <tr>\n", + " <th>9</th>\n", + " <td>Acinetobacter baumannii AB307-0294</td>\n", + " <td>Imipenem</td>\n", + " <td>1</td>\n", + " </tr>\n", + " <tr>\n", + " <th>10</th>\n", + " <td>Acinetobacter baumannii AB307-0294</td>\n", + " <td>Tigecycline</td>\n", + " <td>0.5</td>\n", + " </tr>\n", + " <tr>\n", + " <th>11</th>\n", + " <td>Acinetobacter baumannii AB5075-UW</td>\n", + " <td>Ceftazidime</td>\n", + " <td>>128</td>\n", + " </tr>\n", + " <tr>\n", + " <th>12</th>\n", + " <td>Acinetobacter baumannii AB5075-UW</td>\n", + " <td>Cefepime</td>\n", + " <td>>256</td>\n", + " </tr>\n", + " <tr>\n", + " <th>13</th>\n", + " <td>Acinetobacter baumannii AB5075-UW</td>\n", + " <td>Ciprofloxacin</td>\n", + " <td>>32</td>\n", + " </tr>\n", + " <tr>\n", + " <th>14</th>\n", + " <td>Acinetobacter baumannii DU202</td>\n", + " <td>colistin</td>\n", + " <td></td>\n", + " </tr>\n", + " <tr>\n", + " <th>15</th>\n", + " <td>Acinetobacter baumannii DU202</td>\n", + " <td>Ampicillin/sulbactam</td>\n", + " <td>>=0.3 mg/L</td>\n", + " </tr>\n", + " <tr>\n", + " <th>16</th>\n", + " <td>Acinetobacter baumannii DU202</td>\n", + " <td>ticarcillin/clavulanic acid</td>\n", + " <td>>=128/2</td>\n", + " </tr>\n", + " <tr>\n", + " <th>17</th>\n", + " <td>Acinetobacter baumannii DU202</td>\n", + " <td>piperacillin/tazobactam</td>\n", + " <td>NA</td>\n", + " </tr>\n", + " <tr>\n", + " <th>18</th>\n", + " <td>Acinetobacter baumannii DU202</td>\n", + " <td>trimethoprim/sulfamethoxazole</td>\n", + " <td>8/152</td>\n", + " </tr>\n", + " <tr>\n", + " <th>19</th>\n", + " <td>Acinetobacter baumannii ORAB01</td>\n", + " <td>piperacillin/tazobactam</td>\n", + " <td>>64/4</td>\n", + " </tr>\n", + " <tr>\n", + " <th>20</th>\n", + " <td>Acinetobacter baumannii strain MRSN7100</td>\n", + " <td>amoxicillin/clavulanic acid</td>\n", + " <td>16/8</td>\n", + " </tr>\n", + " <tr>\n", + " <th>21</th>\n", + " <td>Acinetobacter baumannii strain MRSN7168</td>\n", + " <td>amoxicillin/clavulanic acid</td>\n", + " <td>16/8</td>\n", + " </tr>\n", + " <tr>\n", + " <th>22</th>\n", + " <td>Acinetobacter baumannii strain MRSN7336</td>\n", + " <td>amoxicillin/clavulanic acid</td>\n", + " <td>16/8</td>\n", + " </tr>\n", + " <tr>\n", + " <th>23</th>\n", + " <td>Acinetobacter baumannii strain MRSN7834</td>\n", + " <td>amoxicillin/clavulanic acid</td>\n", + " <td>16/8</td>\n", + " </tr>\n", + " <tr>\n", + " <th>24</th>\n", + " <td>Acinetobacter baumannii strain FDA-CDC-AR_0305</td>\n", + " <td>polymyxin B</td>\n", + " <td>1</td>\n", + " </tr>\n", + " <tr>\n", + " <th>25</th>\n", + " <td>Acinetobacter baumannii strain FDA-CDC-AR_0306</td>\n", + " <td>polymyxin B</td>\n", + " <td>1</td>\n", + " </tr>\n", + " <tr>\n", + " <th>26</th>\n", + " <td>Acinetobacter baumannii strain FDA-CDC-AR_0307</td>\n", + " <td>polymyxin B</td>\n", + " <td>8</td>\n", + " </tr>\n", + " <tr>\n", + " <th>27</th>\n", + " <td>Acinetobacter baumannii strain FDA-CDC-AR_0308</td>\n", + " <td>polymyxin B</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 AB307-0294 \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 AB5075-UW \n", + "12 Acinetobacter baumannii AB5075-UW \n", + "13 Acinetobacter baumannii AB5075-UW \n", + "14 Acinetobacter baumannii DU202 \n", + "15 Acinetobacter baumannii DU202 \n", + "16 Acinetobacter baumannii DU202 \n", + "17 Acinetobacter baumannii DU202 \n", + "18 Acinetobacter baumannii DU202 \n", + "19 Acinetobacter baumannii ORAB01 \n", + "20 Acinetobacter baumannii strain MRSN7100 \n", + "21 Acinetobacter baumannii strain MRSN7168 \n", + "22 Acinetobacter baumannii strain MRSN7336 \n", + "23 Acinetobacter baumannii strain MRSN7834 \n", + "24 Acinetobacter baumannii strain FDA-CDC-AR_0305 \n", + "25 Acinetobacter baumannii strain FDA-CDC-AR_0306 \n", + "26 Acinetobacter baumannii strain FDA-CDC-AR_0307 \n", + "27 Acinetobacter baumannii strain FDA-CDC-AR_0308 \n", + "\n", + " Antibiotics MIC \n", + "0 Colistin 0.1 \n", + "1 Netilmicin 1 \n", + "2 Ampicillin 0 \n", + "3 Ampicillin/sulbactam mg/L \n", + "4 piperacillin/tazobactam 0 \n", + "5 Cefazolin 64 \n", + "6 Ceftriaxone 16 \n", + "7 Cefepime 8 \n", + "8 Meropenem 0.25 \n", + "9 Imipenem 1 \n", + "10 Tigecycline 0.5 \n", + "11 Ceftazidime >128 \n", + "12 Cefepime >256 \n", + "13 Ciprofloxacin >32 \n", + "14 colistin \n", + "15 Ampicillin/sulbactam >=0.3 mg/L \n", + "16 ticarcillin/clavulanic acid >=128/2 \n", + "17 piperacillin/tazobactam NA \n", + "18 trimethoprim/sulfamethoxazole 8/152 \n", + "19 piperacillin/tazobactam >64/4 \n", + "20 amoxicillin/clavulanic acid 16/8 \n", + "21 amoxicillin/clavulanic acid 16/8 \n", + "22 amoxicillin/clavulanic acid 16/8 \n", + "23 amoxicillin/clavulanic acid 16/8 \n", + "24 polymyxin B 1 \n", + "25 polymyxin B 1 \n", + "26 polymyxin B 8 \n", + "27 polymyxin B 4 " + ] + }, + "execution_count": 43, + "metadata": {}, + "output_type": "execute_result" + } + ], + "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)\n", + "#strain_mic" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "id": "0d30ddc3", + "metadata": {}, + "outputs": [], + "source": [ + "clsi_bp=pd.read_csv(input_clsi,sep=',')\n", + "\n", + "#clsi_bp[clsi_bp[['Antibiotics', 'Susceptible']].duplicated()].shape" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "id": "a818676d", + "metadata": {}, + "outputs": [], + "source": [ + "#clsi_bp\n", + "#strain_mic" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "id": "c6b4c59b", + "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": 47, + "id": "d0171f94", + "metadata": {}, + "outputs": [], + "source": [ + "#clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))" + ] + }, + { + "cell_type": "code", + "execution_count": 48, + "id": "fe45b2dd", + "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": 49, + "id": "ddbbe4d9", + "metadata": {}, + "outputs": [], + "source": [ + "#strain_mic" + ] + }, + { + "cell_type": "code", + "execution_count": 50, + "id": "640508f1", + "metadata": {}, + "outputs": [], + "source": [ + "# capitalize each Antibiotic Name for comparision with removing whitespace\n", + "strain_mic['Strain name']=strain_mic['Strain name'].str.capitalize().str.replace(\" \",\"\")\n", + "strain_mic['Antibiotics']=strain_mic['Antibiotics'].str.capitalize().str.replace(\" \",\"\")\n", + "\n", + "clsi_bp['Antibiotics']=clsi_bp['Antibiotics'].str.capitalize().str.replace(\" \",\"\")" + ] + }, + { + "cell_type": "code", + "execution_count": 51, + "id": "b87426f4", + "metadata": {}, + "outputs": [], + "source": [ + "#find duplicate values in input files\n", + "dups=strain_mic[strain_mic[['Strain name', 'Antibiotics']].duplicated(keep=False)]\n", + "if dups.shape[0] != 0:\n", + " print ('Please provide a single MIC value in input file for given duplicates combination of \\'Strain name and Antibiotics\\' to use the tool:-\\n',dups)\n", + " #exit()\n", + "else:\n", + " #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')" + ] + }, + { + "cell_type": "code", + "execution_count": 52, + "id": "91bfc94d", + "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>Acinetobacterbaumanniia85</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>Acinetobacterbaumanniidu202</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>2</th>\n", + " <td>Acinetobacterbaumanniia85</td>\n", + " <td>Netilmicin</td>\n", + " <td>1</td>\n", + " <td>1</td>\n", + " <td>8</td>\n", + " <td>32</td>\n", + " <td>16</td>\n", + " </tr>\n", + " <tr>\n", + " <th>3</th>\n", + " <td>Acinetobacterbaumanniiab307-0294</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>4</th>\n", + " <td>Acinetobacterbaumanniidu202</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>5</th>\n", + " <td>Acinetobacterbaumanniiab307-0294</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>6</th>\n", + " <td>Acinetobacterbaumanniidu202</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>7</th>\n", + " <td>Acinetobacterbaumanniiorab01</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>8</th>\n", + " <td>Acinetobacterbaumanniiab307-0294</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>9</th>\n", + " <td>Acinetobacterbaumanniiab307-0294</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>10</th>\n", + " <td>Acinetobacterbaumanniiab5075-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>11</th>\n", + " <td>Acinetobacterbaumanniiab307-0294</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>12</th>\n", + " <td>Acinetobacterbaumanniiab307-0294</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>13</th>\n", + " <td>Acinetobacterbaumanniiab5075-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>14</th>\n", + " <td>Acinetobacterbaumanniiab5075-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>15</th>\n", + " <td>Acinetobacterbaumanniidu202</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>16</th>\n", + " <td>Acinetobacterbaumanniidu202</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>Acinetobacterbaumanniistrainfda-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>18</th>\n", + " <td>Acinetobacterbaumanniistrainfda-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>19</th>\n", + " <td>Acinetobacterbaumanniistrainfda-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>20</th>\n", + " <td>Acinetobacterbaumanniistrainfda-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 Acinetobacterbaumanniia85 \n", + "1 Acinetobacterbaumanniidu202 \n", + "2 Acinetobacterbaumanniia85 \n", + "3 Acinetobacterbaumanniiab307-0294 \n", + "4 Acinetobacterbaumanniidu202 \n", + "5 Acinetobacterbaumanniiab307-0294 \n", + "6 Acinetobacterbaumanniidu202 \n", + "7 Acinetobacterbaumanniiorab01 \n", + "8 Acinetobacterbaumanniiab307-0294 \n", + "9 Acinetobacterbaumanniiab307-0294 \n", + "10 Acinetobacterbaumanniiab5075-uw \n", + "11 Acinetobacterbaumanniiab307-0294 \n", + "12 Acinetobacterbaumanniiab307-0294 \n", + "13 Acinetobacterbaumanniiab5075-uw \n", + "14 Acinetobacterbaumanniiab5075-uw \n", + "15 Acinetobacterbaumanniidu202 \n", + "16 Acinetobacterbaumanniidu202 \n", + "17 Acinetobacterbaumanniistrainfda-cdc-ar_0305 \n", + "18 Acinetobacterbaumanniistrainfda-cdc-ar_0306 \n", + "19 Acinetobacterbaumanniistrainfda-cdc-ar_0307 \n", + "20 Acinetobacterbaumanniistrainfda-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 - 4 2 \n", + "2 Netilmicin 1 1 8 32 16 \n", + "3 Ampicillin/sulbactam mg/L / 8/4 32/16 16/8 \n", + "4 Ampicillin/sulbactam >=0.3 mg/L 0.3/ 8/4 32/16 16/8 \n", + "5 Piperacillin/tazobactam 0 0 16/4 128/4 32/4-64/4 \n", + "6 Piperacillin/tazobactam NA 16/4 128/4 32/4-64/4 \n", + "7 Piperacillin/tazobactam >64/4 64/4 16/4 128/4 32/4-64/4 \n", + "8 Ceftriaxone 16 16 8 64 16-32 \n", + "9 Cefepime 8 8 8 32 16 \n", + "10 Cefepime >256 256 8 32 16 \n", + "11 Meropenem 0.25 0.25 2 8 4 \n", + "12 Imipenem 1 1 2 8 4 \n", + "13 Ceftazidime >128 128 8 32 16 \n", + "14 Ciprofloxacin >32 32 1 4 2 \n", + "15 Ticarcillin/clavulanicacid >=128/2 128/2 16/2 128/2 32/2-64/2 \n", + "16 Trimethoprim/sulfamethoxazole 8/152 8/152 2/38 4/76 - \n", + "17 Polymyxinb 1 1 - 4 2 \n", + "18 Polymyxinb 1 1 - 4 2 \n", + "19 Polymyxinb 8 8 - 4 2 \n", + "20 Polymyxinb 4 4 - 4 2 " + ] + }, + "execution_count": 52, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#result" + ] + }, + { + "cell_type": "code", + "execution_count": 53, + "id": "b171f205", + "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_int,axis = 1)\n", + "#except ValueError:\n", + "# print('Waring: Error in input MIC value')" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "id": "3336fd92", + "metadata": {}, + "outputs": [], + "source": [ + "#result" + ] + }, + { + "cell_type": "code", + "execution_count": 55, + "id": "f0dacfd1", + "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": 56, + "id": "3d8d03f7", + "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": 57, + "id": "7d7223a3", + "metadata": {}, + "outputs": [], + "source": [ + "#result_table" + ] + }, + { + "cell_type": "code", + "execution_count": 58, + "id": "8a41b2ef", + "metadata": {}, + "outputs": [], + "source": [ + "#result_table.to_csv(output_table,na_rep='NA')" + ] + }, + { + "cell_type": "code", + "execution_count": 59, + "id": "8c9e5f87", + "metadata": {}, + "outputs": [], + "source": [ + "# reorder the Antibiotics for ASIST\n", + "clsi_ab=['Amikacin','Tobramycin','Gentamycin','Netilmicin','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": 60, + "id": "cdf43afb", + "metadata": {}, + "outputs": [], + "source": [ + "#print(result_selected.shape, result_table.shape)" + ] + }, + { + "cell_type": "code", + "execution_count": 61, + "id": "c4c4df30", + "metadata": {}, + "outputs": [], + "source": [ + "#result_selected.insert(0,'Resistance_phenotype','')" + ] + }, + { + "cell_type": "code", + "execution_count": 62, + "id": "9adb2703", + "metadata": {}, + "outputs": [], + "source": [ + "#rename headers\n", + "result_selected=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": 63, + "id": "50e6cf5f", + "metadata": {}, + "outputs": [], + "source": [ + "#result_selected" + ] + }, + { + "cell_type": "code", + "execution_count": 64, + "id": "2833671c", + "metadata": {}, + "outputs": [], + "source": [ + "result_selected.to_csv(output_table,na_rep='NA')" + ] + } + ], + "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": "3.7.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}