Mercurial > repos > rakesh4osdd > clsi_profile
changeset 1:c5ffaf5288fe draft
Deleted selected files
| author | rakesh4osdd |
|---|---|
| date | Fri, 11 Jun 2021 13:19:48 +0000 |
| parents | 62226cd1acb5 |
| children | 306236ec0511 |
| files | clsi_profile_type2.py clsi_profile_type2_linux-Copy1.ipynb clsi_profile_type2_linux.ipynb dump/clsi.csv dump/clsi_profile.xml dump/clsi_profile_comb.csv dump/input.csv dump/input_ast_comb2.csv dump/input_ast_comb2.csv_table.csv dump/output.csv |
| diffstat | 10 files changed, 0 insertions(+), 3316 deletions(-) [+] |
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--- a/clsi_profile_type2.py Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,244 +0,0 @@ -#!/usr/bin/env python -# coding: utf-8 - -# In[1245]: - - -# ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics -# By rakesh4osdd@gmail.com, 06-Jun-2021 -import pandas as pd -import re -import sys - - -# In[1246]: - - -# cross check MIC values -def sus_res(mic): - #print(mic) - #print ((mic,pd.isna(mic[1]),pd.isna(mic[0]),'\n') - if not (pd.isna(mic[0]) or pd.isna(mic[1]) or pd.isna(mic[2])):#check for NaN value - #remove unwanted whitespace - o_mic = mic[0].replace(' ', '') - s_mic = mic[1].replace(' ', '') - r_mic = mic[2].replace(' ', '') - #print (o_mic,s_mic,r_mic) - #print (type(o_mic),type(s_mic),type(r_mic)) - if '/' in s_mic: #check for combination antibiotics - #print ('combination antibiotics') - try: - if '/' in o_mic: - #print ('input combination') - if (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(o_mic.split('/')[1]) <= float(s_mic.split('/')[1])): - strain_type='Susceptible' - elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(o_mic.split('/')[1]) >= float(r_mic.split('/')[1])): - strain_type='Resistant' - else: - strain_type='Intermediate' - else: - #print ('single') - if float(o_mic)==0: - strain_type='Strain could not classified' - elif (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(1) <= float(s_mic.split('/')[1])): - strain_type='Susceptible' - elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(1) >= float(r_mic.split('/')[1])): - strain_type='Resistant' - else: - strain_type='Intermediate' - except ValueError: - strain_type='Strain could not classified' - else: #single antibiotics - #print('single antibiotics') - if o_mic: - if float(o_mic)==0: - strain_type='Strain could not classified' - elif (float(o_mic) <= float(s_mic)): - strain_type='Susceptible' - elif (float(o_mic) >= float(r_mic)): - strain_type='Resistant' - else: - strain_type='Intermediate' - else: - strain_type='Strain could not classified' - else: - strain_type='Strain could not classified' - return(strain_type) - - -# In[ ]: - -# for input argument -input_user = sys.argv[1] -input_clsi = sys.argv[2] -output_table = sys.argv[3] - -# In[1247]: - - -""" -input_user='input_ast_comb2.csv' -input_clsi='clsi_profile_comb.csv' -output_profile=input_user+'_profile.csv' -output_table=input_user+'_table.csv' - -""" - -# In[1248]: - - -# read user AST data with selected 3 columns -strain_mic=pd.read_csv(input_user, sep=',', usecols =['Strain name', 'Antibiotics', 'MIC'],na_filter=False) - - -# In[1249]: - - -clsi_bp=pd.read_csv(input_clsi,sep=',') - - -# In[1290]: - - -#clsi_bp.head(2) -#strain_mic - - -# In[1251]: - - -# convert MIC to numbers sMIC, rMIC -clsi_bp['s_mic'] =clsi_bp[['Susceptible']].applymap(lambda x: (re.sub(r'[^0-9.\/]', '', x))) -clsi_bp['r_mic'] =clsi_bp[['Resistant']].applymap(lambda x: (re.sub(r'[^0-9.\/]', '', x))) - - -# In[1252]: - - -# Read only numbers in MIC values -#try: -strain_mic['o_mic']=strain_mic[['MIC']].applymap(lambda x: (re.sub(r'[^0-9.\/]','', x))) -#except TypeError: -# print('Waring: Error in MIC value') - - -# In[1289]: - - -#strain_mic.head() - - -# In[1254]: - - -# capitalize each Antibiotic Name for comparision with removing whitespace -strain_mic['Antibiotics']=strain_mic['Antibiotics'].str.capitalize().str.replace(" ","") -clsi_bp['Antibiotics']=clsi_bp['Antibiotics'].str.capitalize().str.replace(" ","") - - -# In[1255]: - - -#compare CLSI Antibiotics only -#result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner', indicator=True)[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','_merge']] -try: - result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner')[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic']] -except KeyError: - print('Waring: Error in input Values') - - -# In[1256]: - - -#compare MIC values and assign Susceptible and Resistant to Strain -#try: -result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic']].apply(sus_res,axis = 1) -#except ValueError: -# print('Waring: Error in input MIC value') - - -# In[1288]: - - -#result - - -# In[1258]: - - -#result[['Strain name', 'Antibiotics', 'MIC','s_mic','r_mic','CLSI_profile']].to_csv(output_profile,sep=',', index=False, encoding='utf-8-sig') - - -# In[1259]: - - -#create a pivot table for ASIST -table=result[['Strain name', 'Antibiotics','CLSI_profile']].drop_duplicates() -result_table=pd.pivot_table(table, values ='CLSI_profile', index =['Strain name'],columns =['Antibiotics'], aggfunc = lambda x: ' '.join(x)) - - -# In[1261]: - - -result_table - - -# In[1264]: - - -#result_table.to_csv(output_table,na_rep='NA') - - -# In[1282]: - - -# reorder the Antibiotics for ASIST -clsi_ab=['Amikacin','Tobramycin','Gentamycin','Imipenem','Meropenem','Doripenem','Ciprofloxacin','Levofloxacin', - 'Piperacillin/tazobactam','Ticarcillin/clavulanicacid','Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime', - 'Trimethoprim/sulfamethoxazole','Ampicillin/sulbactam','Colistin','Polymyxinb','Tetracycline','Doxicycline ', - 'Minocycline'] -result_selected=result_table.filter(clsi_ab) - - -# In[1283]: - - -result_selected.shape - - -# In[1284]: - - -result_table.shape - - -# In[1285]: - - -result_selected.insert(0,'Resistance_phenotype','') - - -# In[1286]: - - -result_selected.to_csv(output_table,na_rep='NA') - - -# In[1287]: - - -#rename headers -result_selected.rename(columns = {'Ticarcillin/clavulanicacid':'Ticarcillin/clavulanic acid','Piperacillin/tazobactam':'Piperacillin/ tazobactam','Trimethoprim/sulfamethoxazole': 'Trimethoprim/ sulfamethoxazole','Ampicillin/sulbactam':'Ampicillin/ sulbactam', 'Polymyxinb': 'Polymyxin B'} ) - - -# In[ ]: - - - - - -# In[ ]: - - - -
--- a/clsi_profile_type2_linux-Copy1.ipynb Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2461 +0,0 @@ -{ - "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 \u001b[0;34m(\u001b[0m\u001b[0mSeries\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndarray\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mIndex\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3160\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_array\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 3161\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3162\u001b[0m \u001b[0;31m# set column\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36m_setitem_array\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m 3196\u001b[0m )[1]\n\u001b[1;32m 3197\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_check_setitem_copy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3198\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0miloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 3199\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3200\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_setitem_frame\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m__setitem__\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m 690\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 691\u001b[0m \u001b[0miloc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"iloc\"\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0miloc\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 692\u001b[0;31m \u001b[0miloc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_with_indexer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 693\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 694\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_validate_key\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - 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"\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 -}
--- a/clsi_profile_type2_linux.ipynb Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,447 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 206, - "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": 207, - "id": "39e25c15", - "metadata": {}, - "outputs": [], - "source": [ - "#print(pd.__version__, re.__version__)" - ] - }, - { - "cell_type": "code", - "execution_count": 208, - "id": "43115c0a", - "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": 209, - "id": "0448ebf3", - "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": 210, - "id": "7784b77d", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'input_user = sys.argv[1]\\ninput_clsi = sys.argv[2]\\noutput_table = sys.argv[3]'" - ] - }, - "execution_count": 210, - "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": 211, - "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": 212, - "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": 213, - "id": "77135cb7", - "metadata": {}, - "outputs": [], - "source": [ - "clsi_bp=pd.read_csv(input_clsi,sep=',')" - ] - }, - { - "cell_type": "code", - "execution_count": 214, - "id": "2ec1cbec", - "metadata": {}, - "outputs": [], - "source": [ - "#clsi_bp\n", - "#strain_mic" - ] - }, - { - "cell_type": "code", - "execution_count": 215, - "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": 216, - "id": "3eee0538", - "metadata": {}, - "outputs": [], - "source": [ - "#clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))" - ] - }, - { - "cell_type": "code", - "execution_count": 217, - "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": 218, - "id": "942fefb2", - "metadata": {}, - "outputs": [], - "source": [ - "#strain_mic" - ] - }, - { - "cell_type": "code", - "execution_count": 219, - "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": 220, - "id": "ea403928", - "metadata": {}, - "outputs": [], - "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')" - ] - }, - { - "cell_type": "code", - "execution_count": 221, - "id": "44f7e35d", - "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": 222, - "id": "30c2a7a3", - "metadata": {}, - "outputs": [], - "source": [ - "#result" - ] - }, - { - "cell_type": "code", - "execution_count": 223, - "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": 224, - "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": 225, - "id": "df439a58", - "metadata": {}, - "outputs": [], - "source": [ - "#result_table" - ] - }, - { - "cell_type": "code", - "execution_count": 226, - "id": "ee19e872", - "metadata": {}, - "outputs": [], - "source": [ - "#result_table.to_csv(output_table,na_rep='NA')" - ] - }, - { - "cell_type": "code", - "execution_count": 227, - "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": 228, - "id": "e0d983b9", - "metadata": {}, - "outputs": [], - "source": [ - "#print(result_selected.shape, result_table.shape)" - ] - }, - { - "cell_type": "code", - "execution_count": 229, - "id": "1b0a4d77", - "metadata": {}, - "outputs": [], - "source": [ - "result_selected.insert(0,'Resistance_phenotype','')" - ] - }, - { - "cell_type": "code", - "execution_count": 230, - "id": "5c162c07", - "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": 231, - "id": "00cd53d4", - "metadata": {}, - "outputs": [], - "source": [ - "#result_selected" - ] - }, - { - "cell_type": "code", - "execution_count": 232, - "id": "d36dcdab", - "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": "3.9.1" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -}
--- a/dump/clsi.csv Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -Antibiotics,Susceptible,Resistant -Amikacin,≤ 16,≥ 64 -Tobramycin,≤ 4,≥ 16 -Gentamicin,≤ 4,≥ 16 -Netilmicin,≤ 8,≥ 32 -Imipenem,≤ 2,≥ 8 -Meropenem,≤ 2,≥ 8 -Doripenem,≤ 2,≥ 8 -Ciprofloxacin,≤ 1,≥ 4 -Levofloxacin,≤ 2,≥ 8 -Piperacillin/ tazobactam,≤ 16/4,≥ 128/4 -Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2 -Cefotaxime,≤ 8,≥ 64 -Ceftriaxone,≤ 8,≥ 64 -Ceftazidime,≤ 8,≥ 32 -Cefepime,≤ 8,≥ 32 -Trimethoprim/ sulfamethoxazole,≤ 2/38,≥ 4/76 -Ampicillin/ sulbactam,≤ 8/4,≥ 32/16 -Colistin,≤ 2,≥ 4 -Polymyxin B,≤ 2,≥ 4 -Tetracycline,≤ 4,≥ 16 -Doxycycline,≤ 4,≥ 16 -Minocycline,≤ 4,≥ 16 \ No newline at end of file
--- a/dump/clsi_profile.xml Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -<tool id="clsi_profile" name="CLSI Profile" version="0.1.0" python_template_version="3.5"> - <description>MIC profile using CLSI MIC breakpoints</description> - - <command detect_errors="exit_code"><![CDATA[ - python '$__tool_directory__/clsi_profile.py' '$input1' '$input2' '$output1' - ]]></command> - <inputs> - <param type="data" name="input1" format="csv" /> - <param type="data" name="input2" format="csv" /> - </inputs> - <outputs> - <data name="output1" format="csv" /> - </outputs> - <tests> - <test> - <param name="input1" value="input.csv"/> - <param name="input2" value="clsi.csv"/> - <output name="output1" file="output.csv"/> - </test> - </tests> - <help><![CDATA[ - Examples Files: - **CLSI MIC breakpoint file example:** :: - - Antibiotics,Susceptible,Resistant,Intermediate - Amikacin,≤ 16,≥ 64,32 - Tobramycin,≤ 4,≥ 16,8 - Gentamicin,≤ 4,≥ 16,8 - - **AST MIC value file example:** :: - Strain name,Antibiotics,MIC - Strain1,Amikacin,≤ 16 - Strain2,Tobramycin,≤ 4 - Strain3,Gentamicin,≤ 4 - ]]></help> -</tool>
--- a/dump/clsi_profile_comb.csv Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -Antibiotics,Susceptible,Resistant -Amikacin,≤ 16,≥ 64 -Tobramycin,≤ 4,≥ 16 -Gentamicin,≤ 4,≥ 16 -Netilmicin,≤ 8,≥ 32 -Imipenem,≤ 2,≥ 8 -Meropenem,≤ 2,≥ 8 -Doripenem,≤ 2,≥ 8 -Ciprofloxacin,≤ 1,≥ 4 -Levofloxacin,≤ 2,≥ 8 -Piperacillin/ tazobactam,≤ 16/4,≥ 128/4 -Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2 -Cefotaxime,≤ 8,≥ 64 -Ceftriaxone,≤ 8,≥ 64 -Ceftazidime,≤ 8,≥ 32 -Cefepime,≤ 8,≥ 32 -Trimethoprim/ sulfamethoxazole,≤ 2/38,≥ 4/76 -Ampicillin/ sulbactam,≤ 8/4,≥ 32/16 -Colistin,≤ 2,≥ 4 -Polymyxin B,≤ 2,≥ 4 -Tetracycline,≤ 4,≥ 16 -Doxycycline,≤ 4,≥ 16 -Minocycline,≤ 4,≥ 16 \ No newline at end of file
--- a/dump/input.csv Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -id,genome Ids,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit -470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L -470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,1,mg/L -470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,2,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L -470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L -470,CP008706.1,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L -470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L -470,CP015483.1,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L -470,470.7601,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.7651,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.7764,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.8071,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.7405,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L -470,470.7406,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L -470,470.7407,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L -470,470.7408,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
--- a/dump/input_ast_comb2.csv Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -id,genome Ids,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit -470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L -470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,1,mg/L -470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,2,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L -470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L -470,CP008706.1,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L -470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L -470,CP015483.1,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L -470,470.7601,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.7651,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.7764,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.8071,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.7405,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L -470,470.7406,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L -470,470.7407,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L -470,470.7408,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
--- a/dump/input_ast_comb2.csv_table.csv Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -Strain name,Resistance_phenotype,Imipenem,Meropenem,Ciprofloxacin,Piperacillin/tazobactam,Ticarcillin/clavulanicacid,Ceftriaxone,Ceftazidime,Cefepime,Trimethoprim/sulfamethoxazole,Ampicillin/sulbactam,Colistin,Polymyxinb -Acinetobacter baumannii A85,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible,NA -Acinetobacter baumannii AB307-0294,,Susceptible,Susceptible,NA,Strain could not classified,NA,Intermediate,NA,Susceptible,NA,Strain could not classified,NA,NA -Acinetobacter baumannii AB5075-UW,,NA,NA,Resistant,NA,NA,NA,Resistant,Resistant,NA,NA,NA,NA -Acinetobacter baumannii DU202,,NA,NA,NA,Strain could not classified,Resistant,NA,NA,NA,Resistant,Strain could not classified,Strain could not classified,NA -Acinetobacter baumannii ORAB01,,NA,NA,NA,Intermediate,NA,NA,NA,NA,NA,NA,NA,NA -Acinetobacter baumannii strain FDA-CDC-AR_0305,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible -Acinetobacter baumannii strain FDA-CDC-AR_0306,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible -Acinetobacter baumannii strain FDA-CDC-AR_0307,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant -Acinetobacter baumannii strain FDA-CDC-AR_0308,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant
--- a/dump/output.csv Fri Jun 11 12:36:25 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -Strain name,Resistance_phenotype,Imipenem,Meropenem,Ciprofloxacin,Piperacillin/tazobactam,Ticarcillin/clavulanicacid,Ceftriaxone,Ceftazidime,Cefepime,Trimethoprim/sulfamethoxazole,Ampicillin/sulbactam,Colistin,Polymyxinb -Acinetobacter baumannii A85,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible,NA -Acinetobacter baumannii AB307-0294,,Susceptible,Susceptible,NA,Strain could not classified,NA,Intermediate,NA,Susceptible,NA,Strain could not classified,NA,NA -Acinetobacter baumannii AB5075-UW,,NA,NA,Resistant,NA,NA,NA,Resistant,Resistant,NA,NA,NA,NA -Acinetobacter baumannii DU202,,NA,NA,NA,Strain could not classified,Resistant,NA,NA,NA,Resistant,Strain could not classified,Strain could not classified,NA -Acinetobacter baumannii ORAB01,,NA,NA,NA,Intermediate,NA,NA,NA,NA,NA,NA,NA,NA -Acinetobacter baumannii strain FDA-CDC-AR_0305,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible -Acinetobacter baumannii strain FDA-CDC-AR_0306,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible -Acinetobacter baumannii strain FDA-CDC-AR_0307,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant -Acinetobacter baumannii strain FDA-CDC-AR_0308,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant