Mercurial > repos > rakesh4osdd > asist
changeset 3:734777d3c253 draft
Deleted selected files test
| author | rakesh4osdd |
|---|---|
| date | Wed, 30 Jun 2021 05:35:56 +0000 |
| parents | 62afd73a0987 |
| children | 3ea72fb2eaac |
| files | LICENSE README.rst asist_dynamic.py clsi_profile.py clsi_profile_type2.py clsi_profile_type2_linux-Copy1.ipynb clsi_profile_type2_linux.ipynb input.csv_table.csv output.csv suite_config.xml tool.sh |
| diffstat | 11 files changed, 47 insertions(+), 4135 deletions(-) [+] |
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--- a/LICENSE Mon Jun 28 15:05:17 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2021 RAKESH KUMAR - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE.
--- a/README.rst Mon Jun 28 15:05:17 2021 +0000 +++ b/README.rst Wed Jun 30 05:35:56 2021 +0000 @@ -2,7 +2,7 @@ CLSI profile for ASIST using the CLSI standards 2020 by AST profiling for bacteria. It help to generate the input file for ASIST program based on MIC values provided by CLSI based AST profiling. -# ASIST: Antimicrobial Susceptibility standards** +# ASIST: Antimicrobial Susceptibility standards In the first column strain names will be mentioned, the second column will be left blank for getting resistance phenotype, starting two rows will comprise antibiotic names (first row) and antibiotic classes (second row). The data for the resistance profile will then start from the C3 column of an excel file which can be converted into a .csv file. Since B3 is left blank, after implementing the algorithm, column B3 will be filled with the resistance phenotype (susceptible, MDR, XDR, PDR). @@ -12,7 +12,7 @@ Strain_1,Phenotype_1,Resistant,Resistant,Resistant Strain_2,Phenotype_2,Resistant,Susceptible,Resistant - Link to the code : https://github.com/rakesh4osdd/asist + Link to the code : https://github.com/rakesh4osdd/clsi_profile , https://github.com/rakesh4osdd/asist # ASIST tool suite
--- a/asist_dynamic.py Mon Jun 28 15:05:17 2021 +0000 +++ b/asist_dynamic.py Wed Jun 30 05:35:56 2021 +0000 @@ -9,7 +9,7 @@ # rakesh4osdd@gmail.com, 14-June-2021 -# In[1403]: +# In[1]: import pandas as pd @@ -18,18 +18,20 @@ from collections import Counter -# In[ ]: +# In[176]: input_file=sys.argv[1] output_file=sys.argv[2] +#input_file='test-data/asist_input.csv' +#output_file='test-data/asist_output.csv' -# In[1362]: +# In[177]: # strain_profile to phenotype condition -def s_phen(sus,res,na,pb_sus): +def s_phen(sus,res,intm,na,pb_sus): if (sus>0 and res==0 and na>=0): #print('Possible Susceptible') phen='Possible Susceptible' @@ -52,13 +54,13 @@ phen='Possible TDR' else: #print('Strain could not be classified') - phen='Strain could not be classified' + phen='Strain could not be classified ('+ str(intm)+' | ' + str(na) +')' return(phen) #print(s_phen(1,9,0,0)) -# In[1363]: +# In[178]: # define Antibiotic groups as per antibiotic of CLSI breakpoints MIC @@ -90,9 +92,10 @@ #print(cats[cat]) cats[cat]=pd_series.filter(cats[cat]) #print(cats[cat]) - #define res,sus,na,pb_sus + #define res,sus,intm,na,pb_sus res=0 sus=0 + intm=0 na=0 pb_sus=0 # special case of 'Polymyxin b' for its value @@ -119,13 +122,16 @@ res=res+1 if k['susceptible']>=1: sus=sus+1 + if k['intermediate']>=1: + intm=intm+1 if k['na']>=1: na=na+1 - #print(s_phen(sus,res,na,pb_sus)) - return(s_phen(sus,res,na,pb_sus)) + #print(sus,res,intm,na,pb_sus) + #print(s_phen(sus,res,intm,na,pb_sus)) + return(s_phen(sus,res,intm,na,pb_sus)) -# In[1397]: +# In[179]: #input_file='input2.csv_table.csv' @@ -133,14 +139,14 @@ strain_profile=pd.read_csv(input_file, sep=',',na_filter=False,skipinitialspace = True) -# In[1387]: +# In[180]: old_strain_name=strain_profile.columns[0] new_strain_name=old_strain_name.capitalize().strip().replace(' ', '') -# In[1388]: +# In[181]: # make header capitalization, remove leading,lagging, and multiple whitespace for comparision @@ -150,7 +156,7 @@ #strain_profile.columns -# In[1389]: +# In[182]: # add new column in dataframe on second position @@ -158,33 +164,54 @@ #strain_profile.head() -# In[1390]: +# In[183]: strain_profile['Strain phenotype'] = strain_profile.apply(lambda x: (s_profiler(x)), axis=1) -# In[1391]: +# In[184]: #strain_profile.head() -# In[1392]: +# In[185]: #rename headers for old name strain_profile=strain_profile.rename(columns = {new_strain_name:old_strain_name, 'Ticarcillin/clavulanicacid':'Ticarcillin/ clavulanic acid','Piperacillin/tazobactam':'Piperacillin/ tazobactam','Trimethoprim/sulfamethoxazole': 'Trimethoprim/ sulfamethoxazole','Ampicillin/sulbactam':'Ampicillin/ sulbactam', 'Polymyxinb': 'Polymyxin B'} ) -# In[1404]: +# In[186]: + + +#strain_profile.columns + + +# In[187]: #strain_profile -# In[1394]: +# In[188]: strain_profile.to_csv(output_file,na_rep='NA',index=False) + +# In[189]: + + +# Open a file with access mode 'a' +with open(output_file, "a") as file_object: + # Append 'hello' at the end of file + file_object.write("Note: \n1. 'MDR': Multidrug-resistant, 'XDR': Extensively drug-resistant, 'TDR':totally drug resistant, NA': Data Not Available.\n2. 'Strain could not be classified' numbers follow the format as ('Number of antibiotics categories count as Intermediate' | 'Number of antibiotics categories count as NA')") + + +# In[ ]: + + + +
--- a/clsi_profile.py Mon Jun 28 15:05:17 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,305 +0,0 @@ -#!/usr/bin/env python -# coding: utf-8 - -# In[206]: - - -# 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[207]: - - -#print(pd.__version__, re.__version__) - - -# In[208]: - - -# compare two MIC value strings -def check_mic(mic1,mic2,mic_type): - #print(mic1,mic2,mic_type) - try: - if '/' in mic1: - m1a = mic1.split('/')[0] - m1b = mic1.split('/')[1] - if float(m1a)==0 or float(m1b)==0: - strain_type='Strain could not be classified' - return(strain_type) - elif '/' in mic2: - m1a = mic1 - if float(m1a)==0: - strain_type='Strain could not be classified' - return(strain_type) - m1b = '1' - elif float(mic1)==0: - strain_type='Strain could not be classified' - return(strain_type) - else: - m1a = mic1 - - if '-' in mic2: - m2a = mic2.split('-')[0] - m2b = mic2.split('-')[1] - - except ValueError: - strain_type='Strain could not be classified' - return(strain_type) - try: - if '-' in mic2 and mic_type == 'i': # for intermediate only - if '/' in mic2: - m2a = mic2.split('-')[0].split('/')[0] - m2b = mic2.split('-')[0].split('/')[1] - m2aa = mic2.split('-')[1].split('/')[0] - m2bb = mic2.split('-')[1].split('/')[1] - if (float(m2aa)>=float(m1a)>=float(m2a) and float(m2bb)>=float(m1b)>=float(m2b)): - #print('intermediate') - m_type='Intermediate' - else: - #print('not define') - m_type='Strain could not be classified' - else: - m2a = mic2.split('-')[0] - m2b = mic2.split('-')[1] - if (float(m2b)>=float(m1a)>=float(m2a)): - #print('intermediate') - m_type='Intermediate' - else: - #print('not define') - m_type='Strain could not be classified' - #print (m1a,m1b,m2a,m2b,m2aa,m2bb) - elif '/' in mic2: - m2a = mic2.split('/')[0] - m2b = mic2.split('/')[1] - #print(m1a,m1b,m2a,m2b,mic_type) - if (mic_type=='s' and (float(m1a)<=float(m2a) and float(m1b)<=float(m2b))): - m_type='Susceptible' - elif (mic_type=='r' and (float(m1a)>=float(m2a) and float(m1b)>=float(m2b))): - m_type='Resistant' - elif (mic_type=='i' and (float(m1a)==float(m2a) and float(m1b)==float(m2b))): - m_type='Intermediate' - else: - m_type='Strain could not be classified' - elif '-' in mic2: - m_type='Strain could not be classified' - else: - m2a=mic2 - if (mic_type=='s' and (float(m1a)<=float(m2a))): - m_type='Susceptible' - elif (mic_type=='r' and (float(m1a)>=float(m2a))): - m_type='Resistant' - elif (mic_type=='i' and (float(m1a)==float(m2a))): - m_type='Intermediate' - else: - m_type='Strain could not be classified-1' - except IndexError: - strain_type='Strain could not be classified-2' - return(strain_type) - - return(m_type) - -#check_mic('65','32-64','i') - - -# In[209]: - - -# compare MIC value in pandas list -def sus_res_int(mic): - #print(mic) - o_mic = mic[0].replace(' ', '') - s_mic = mic[1].replace(' ', '') - r_mic = mic[2].replace(' ', '') - i_mic = mic[3].replace(' ', '') - try: - if check_mic(o_mic,s_mic,'s')=='Susceptible': - strain_type='Susceptible' - elif check_mic(o_mic,r_mic,'r')=='Resistant': - strain_type='Resistant' - elif check_mic(o_mic,i_mic,'i')=='Intermediate': - strain_type='Intermediate' - else: - strain_type='Strain could not be classified' - except ValueError: - strain_type='Strain could not be classified' - return(strain_type) - -#mic=['128','16/4','128/4','32/4-64/4'] -#sus_res_int(mic) - - -# In[210]: - - -# for input argument -input_user = sys.argv[1] -input_clsi = sys.argv[2] -output_table = sys.argv[3] - - -# In[211]: - -""" -input_user='input.csv' -input_clsi='clsi.csv' -output_profile=input_user+'_profile.csv' -output_table=input_user+'_table.csv' -""" - -# In[212]: - - -# 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[213]: - - -clsi_bp=pd.read_csv(input_clsi,sep=',') - - -# In[214]: - - -#clsi_bp -#strain_mic - - -# In[215]: - - -# 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))) -clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\/-]', '', x))) - - -# In[216]: - - -#clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\/-]', '', x))) - - -# In[217]: - - -# 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[218]: - - -#strain_mic - - -# In[219]: - - -# 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[220]: - - -#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','i_mic']] -except KeyError: - print('Waring: Error in input Values') - - -# In[221]: - - -#compare MIC values and assign Susceptible and Resistant to Strain -#try: -result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res_int,axis = 1) -#except ValueError: -# print('Waring: Error in input MIC value') - - -# In[222]: - - -#result - - -# In[223]: - - -#result[['Strain name', 'Antibiotics', 'MIC','s_mic','r_mic','CLSI_profile']].to_csv(output_profile,sep=',', index=False, encoding='utf-8-sig') - - -# In[224]: - - -#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[225]: - - -#result_table - - -# In[226]: - - -#result_table.to_csv(output_table,na_rep='NA') - - -# In[227]: - - -# 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[228]: - - -#print(result_selected.shape, result_table.shape) - - -# In[229]: - - -#result_selected.insert(0,'Resistance_phenotype','') - - -# In[230]: - - -#rename headers -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'} ) - - -# In[231]: - - -#result_selected - - -# In[232]: - - -result_selected.to_csv(output_table,na_rep='NA') -
--- a/clsi_profile_type2.py Mon Jun 28 15:05:17 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 Mon Jun 28 15:05:17 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", - 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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 Mon Jun 28 15:05:17 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1040 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 37, - "id": "9aa0a6f7", - "metadata": {}, - "outputs": [], - "source": [ - "# ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics\n", - "# By rakesh4osdd@gmail.com, 06-Jun-2021\n", - "import pandas as pd\n", - "import re\n", - "import sys" - ] - }, - { - "cell_type": "code", - "execution_count": 38, - "id": "9af8387e", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "1.2.4 2.2.1\n" - ] - } - ], - "source": [ - "#print(pd.__version__, re.__version__)" - ] - }, - { - "cell_type": "code", - "execution_count": 39, - "id": "73d0783c", - "metadata": {}, - "outputs": [], - "source": [ - "# compare two MIC value strings\n", - "def check_mic(mic1,mic2,mic_type):\n", - " #print(mic1,mic2,mic_type)\n", - " try:\n", - " if '/' in mic1:\n", - " m1a = mic1.split('/')[0]\n", - " m1b = mic1.split('/')[1]\n", - " if float(m1a)==0 or float(m1b)==0:\n", - " strain_type='Strain could not be classified'\n", - " return(strain_type) \n", - " elif '/' in mic2:\n", - " m1a = mic1\n", - " if float(m1a)==0:\n", - " strain_type='Strain could not be classified'\n", - " return(strain_type) \n", - " m1b = '1'\n", - " elif float(mic1)==0:\n", - " strain_type='Strain could not be classified'\n", - " return(strain_type)\n", - " else:\n", - " m1a = mic1\n", - " \n", - " if '-' in mic2:\n", - " m2a = mic2.split('-')[0]\n", - " m2b = mic2.split('-')[1] \n", - " \n", - " except ValueError:\n", - " strain_type='Strain could not be classified' \n", - " return(strain_type)\n", - " try:\n", - " if '-' in mic2 and mic_type == 'i': # for intermediate only\n", - " if '/' in mic2:\n", - " m2a = mic2.split('-')[0].split('/')[0]\n", - " m2b = mic2.split('-')[0].split('/')[1]\n", - " m2aa = mic2.split('-')[1].split('/')[0]\n", - " m2bb = mic2.split('-')[1].split('/')[1]\n", - " if (float(m2aa)>=float(m1a)>=float(m2a) and float(m2bb)>=float(m1b)>=float(m2b)):\n", - " #print('intermediate')\n", - " m_type='Intermediate'\n", - " else:\n", - " #print('not define')\n", - " m_type='Strain could not be classified'\n", - " else:\n", - " m2a = mic2.split('-')[0]\n", - " m2b = mic2.split('-')[1] \n", - " if (float(m2b)>=float(m1a)>=float(m2a)):\n", - " #print('intermediate')\n", - " m_type='Intermediate'\n", - " else:\n", - " #print('not define')\n", - " m_type='Strain could not be classified' \n", - " #print (m1a,m1b,m2a,m2b,m2aa,m2bb)\n", - " elif '/' in mic2:\n", - " m2a = mic2.split('/')[0]\n", - " m2b = mic2.split('/')[1]\n", - " #print(m1a,m1b,m2a,m2b,mic_type)\n", - " if (mic_type=='s' and (float(m1a)<=float(m2a) and float(m1b)<=float(m2b))):\n", - " m_type='Susceptible'\n", - " elif (mic_type=='r' and (float(m1a)>=float(m2a) and float(m1b)>=float(m2b))):\n", - " m_type='Resistant'\n", - " elif (mic_type=='i' and (float(m1a)==float(m2a) and float(m1b)==float(m2b))):\n", - " m_type='Intermediate'\n", - " else:\n", - " m_type='Strain could not be classified'\n", - " elif '-' in mic2:\n", - " m_type='Strain could not be classified'\n", - " else:\n", - " m2a=mic2\n", - " if (mic_type=='s' and (float(m1a)<=float(m2a))):\n", - " m_type='Susceptible'\n", - " elif (mic_type=='r' and (float(m1a)>=float(m2a))):\n", - " m_type='Resistant'\n", - " elif (mic_type=='i' and (float(m1a)==float(m2a))):\n", - " m_type='Intermediate'\n", - " else:\n", - " m_type='Strain could not be classified-1' \n", - " except IndexError:\n", - " strain_type='Strain could not be classified-2' \n", - " return(strain_type)\n", - " \n", - " return(m_type)\n", - "\n", - "#check_mic('65','32-64','i')" - ] - }, - { - "cell_type": "code", - "execution_count": 40, - "id": "4d2ab1b1", - "metadata": {}, - "outputs": [], - "source": [ - "# compare MIC value in pandas list\n", - "def sus_res_int(mic):\n", - " #print(mic)\n", - " o_mic = mic[0].replace(' ', '')\n", - " s_mic = mic[1].replace(' ', '')\n", - " r_mic = mic[2].replace(' ', '')\n", - " i_mic = mic[3].replace(' ', '')\n", - " try:\n", - " if check_mic(o_mic,s_mic,'s')=='Susceptible':\n", - " strain_type='Susceptible'\n", - " elif check_mic(o_mic,r_mic,'r')=='Resistant':\n", - " strain_type='Resistant'\n", - " elif check_mic(o_mic,i_mic,'i')=='Intermediate':\n", - " strain_type='Intermediate' \n", - " else:\n", - " strain_type='Strain could not be classified'\n", - " except ValueError:\n", - " strain_type='Strain could not be classified' \n", - " return(strain_type)\n", - "\n", - "#mic=['128','16/4','128/4','32/4-64/4']\n", - "#sus_res_int(mic)" - ] - }, - { - "cell_type": "code", - "execution_count": 41, - "id": "0e22ef0d", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'# for input argument\\ninput_user = sys.argv[1]\\ninput_clsi = sys.argv[2]\\noutput_table = sys.argv[3]'" - ] - }, - "execution_count": 41, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# for input argument\n", - "input_user = sys.argv[1]\n", - "input_clsi = sys.argv[2]\n", - "output_table = sys.argv[3]" - ] - }, - { - "cell_type": "code", - "execution_count": 42, - "id": "21d5fe63", - "metadata": {}, - "outputs": [], - "source": [ - "'''input_user='input2.csv'\n", - "input_clsi='clsi.csv'\n", - "output_profile=input_user+'_profile.csv'\n", - "output_table=input_user+'_table.csv''''" - ] - }, - { - "cell_type": "code", - "execution_count": 43, - "id": "1e64b025", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "<div>\n", - "<style scoped>\n", - " .dataframe tbody tr th:only-of-type {\n", - " vertical-align: middle;\n", - " }\n", - "\n", - " .dataframe tbody tr th {\n", - " vertical-align: top;\n", - " }\n", - "\n", - " .dataframe thead th {\n", - " text-align: right;\n", - " }\n", - "</style>\n", - "<table border=\"1\" class=\"dataframe\">\n", - " <thead>\n", - " <tr style=\"text-align: right;\">\n", - " <th></th>\n", - " <th>Strain name</th>\n", - " <th>Antibiotics</th>\n", - " <th>MIC</th>\n", - " </tr>\n", - " </thead>\n", - " <tbody>\n", - " <tr>\n", - " <th>0</th>\n", - " <td>Acinetobacter baumannii A85</td>\n", - " <td>Colistin</td>\n", - " <td>0.1</td>\n", - " </tr>\n", - " <tr>\n", - " <th>1</th>\n", - " <td>Acinetobacter baumannii A85</td>\n", - " <td>Netilmicin</td>\n", - " <td>1</td>\n", - " </tr>\n", - " <tr>\n", - " <th>2</th>\n", - " <td>Acinetobacter baumannii AB307-0294</td>\n", - " <td>Ampicillin</td>\n", - " <td>0</td>\n", - " </tr>\n", - " <tr>\n", - " <th>3</th>\n", - " <td>Acinetobacter baumannii AB307-0294</td>\n", - " <td>Ampicillin/sulbactam</td>\n", - " <td>mg/L</td>\n", - " </tr>\n", - " <tr>\n", - " <th>4</th>\n", - " <td>Acinetobacter baumannii AB307-0294</td>\n", - " <td>piperacillin/tazobactam</td>\n", - " <td>0</td>\n", - " </tr>\n", - " <tr>\n", - " <th>5</th>\n", - " <td>Acinetobacter baumannii AB307-0294</td>\n", - " <td>Cefazolin</td>\n", - " <td>64</td>\n", - " </tr>\n", - " <tr>\n", - " <th>6</th>\n", - " <td>Acinetobacter baumannii AB307-0294</td>\n", - " <td>Ceftriaxone</td>\n", - " <td>16</td>\n", - " </tr>\n", - " <tr>\n", - " <th>7</th>\n", - " <td>Acinetobacter baumannii AB307-0294</td>\n", - " <td>Cefepime</td>\n", - " <td>8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>8</th>\n", - " <td>Acinetobacter baumannii AB307-0294</td>\n", - " <td>Meropenem</td>\n", - " <td>0.25</td>\n", - " </tr>\n", - " <tr>\n", - " <th>9</th>\n", - " <td>Acinetobacter baumannii AB307-0294</td>\n", - " <td>Imipenem</td>\n", - " <td>1</td>\n", - " </tr>\n", - " <tr>\n", - " <th>10</th>\n", - " <td>Acinetobacter baumannii AB307-0294</td>\n", - " <td>Tigecycline</td>\n", - " <td>0.5</td>\n", - " </tr>\n", - " <tr>\n", - " <th>11</th>\n", - " <td>Acinetobacter baumannii AB5075-UW</td>\n", - " <td>Ceftazidime</td>\n", - " <td>>128</td>\n", - " </tr>\n", - " <tr>\n", - " <th>12</th>\n", - " <td>Acinetobacter baumannii AB5075-UW</td>\n", - " <td>Cefepime</td>\n", - " <td>>256</td>\n", - " </tr>\n", - " <tr>\n", - " <th>13</th>\n", - " <td>Acinetobacter baumannii AB5075-UW</td>\n", - " <td>Ciprofloxacin</td>\n", - " <td>>32</td>\n", - " </tr>\n", - " <tr>\n", - " <th>14</th>\n", - " <td>Acinetobacter baumannii DU202</td>\n", - " <td>colistin</td>\n", - " <td></td>\n", - " </tr>\n", - " <tr>\n", - " <th>15</th>\n", - " <td>Acinetobacter baumannii DU202</td>\n", - " <td>Ampicillin/sulbactam</td>\n", - " <td>>=0.3 mg/L</td>\n", - " </tr>\n", - " <tr>\n", - " <th>16</th>\n", - " <td>Acinetobacter baumannii DU202</td>\n", - " <td>ticarcillin/clavulanic acid</td>\n", - " <td>>=128/2</td>\n", - " </tr>\n", - " <tr>\n", - " <th>17</th>\n", - " <td>Acinetobacter baumannii DU202</td>\n", - " <td>piperacillin/tazobactam</td>\n", - " <td>NA</td>\n", - " </tr>\n", - " <tr>\n", - " <th>18</th>\n", - " <td>Acinetobacter baumannii DU202</td>\n", - " <td>trimethoprim/sulfamethoxazole</td>\n", - " <td>8/152</td>\n", - " </tr>\n", - " <tr>\n", - " <th>19</th>\n", - " <td>Acinetobacter baumannii ORAB01</td>\n", - " <td>piperacillin/tazobactam</td>\n", - " <td>>64/4</td>\n", - " </tr>\n", - " <tr>\n", - " <th>20</th>\n", - " <td>Acinetobacter baumannii strain MRSN7100</td>\n", - " <td>amoxicillin/clavulanic acid</td>\n", - " <td>16/8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>21</th>\n", - " <td>Acinetobacter baumannii strain MRSN7168</td>\n", - " <td>amoxicillin/clavulanic acid</td>\n", - " <td>16/8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>22</th>\n", - " <td>Acinetobacter baumannii strain MRSN7336</td>\n", - " <td>amoxicillin/clavulanic acid</td>\n", - " <td>16/8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>23</th>\n", - " <td>Acinetobacter baumannii strain MRSN7834</td>\n", - " <td>amoxicillin/clavulanic acid</td>\n", - " <td>16/8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>24</th>\n", - " <td>Acinetobacter baumannii strain FDA-CDC-AR_0305</td>\n", - " <td>polymyxin B</td>\n", - " <td>1</td>\n", - " </tr>\n", - " <tr>\n", - " <th>25</th>\n", - " <td>Acinetobacter baumannii strain FDA-CDC-AR_0306</td>\n", - " <td>polymyxin B</td>\n", - " <td>1</td>\n", - " </tr>\n", - " <tr>\n", - " <th>26</th>\n", - " <td>Acinetobacter baumannii strain FDA-CDC-AR_0307</td>\n", - " <td>polymyxin B</td>\n", - " <td>8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>27</th>\n", - " <td>Acinetobacter baumannii strain FDA-CDC-AR_0308</td>\n", - " <td>polymyxin B</td>\n", - " <td>4</td>\n", - " </tr>\n", - " </tbody>\n", - "</table>\n", - "</div>" - ], - "text/plain": [ - " Strain name \\\n", - "0 Acinetobacter baumannii A85 \n", - "1 Acinetobacter baumannii A85 \n", - "2 Acinetobacter baumannii AB307-0294 \n", - "3 Acinetobacter baumannii AB307-0294 \n", - "4 Acinetobacter baumannii AB307-0294 \n", - "5 Acinetobacter baumannii AB307-0294 \n", - "6 Acinetobacter baumannii AB307-0294 \n", - "7 Acinetobacter baumannii AB307-0294 \n", - "8 Acinetobacter baumannii AB307-0294 \n", - "9 Acinetobacter baumannii AB307-0294 \n", - "10 Acinetobacter baumannii AB307-0294 \n", - "11 Acinetobacter baumannii AB5075-UW \n", - "12 Acinetobacter baumannii AB5075-UW \n", - "13 Acinetobacter baumannii AB5075-UW \n", - "14 Acinetobacter baumannii DU202 \n", - "15 Acinetobacter baumannii DU202 \n", - "16 Acinetobacter baumannii DU202 \n", - "17 Acinetobacter baumannii DU202 \n", - "18 Acinetobacter baumannii DU202 \n", - "19 Acinetobacter baumannii ORAB01 \n", - "20 Acinetobacter baumannii strain MRSN7100 \n", - "21 Acinetobacter baumannii strain MRSN7168 \n", - "22 Acinetobacter baumannii strain MRSN7336 \n", - "23 Acinetobacter baumannii strain MRSN7834 \n", - "24 Acinetobacter baumannii strain FDA-CDC-AR_0305 \n", - "25 Acinetobacter baumannii strain FDA-CDC-AR_0306 \n", - "26 Acinetobacter baumannii strain FDA-CDC-AR_0307 \n", - "27 Acinetobacter baumannii strain FDA-CDC-AR_0308 \n", - "\n", - " Antibiotics MIC \n", - "0 Colistin 0.1 \n", - "1 Netilmicin 1 \n", - "2 Ampicillin 0 \n", - "3 Ampicillin/sulbactam mg/L \n", - "4 piperacillin/tazobactam 0 \n", - "5 Cefazolin 64 \n", - "6 Ceftriaxone 16 \n", - "7 Cefepime 8 \n", - "8 Meropenem 0.25 \n", - "9 Imipenem 1 \n", - "10 Tigecycline 0.5 \n", - "11 Ceftazidime >128 \n", - "12 Cefepime >256 \n", - "13 Ciprofloxacin >32 \n", - "14 colistin \n", - "15 Ampicillin/sulbactam >=0.3 mg/L \n", - "16 ticarcillin/clavulanic acid >=128/2 \n", - "17 piperacillin/tazobactam NA \n", - "18 trimethoprim/sulfamethoxazole 8/152 \n", - "19 piperacillin/tazobactam >64/4 \n", - "20 amoxicillin/clavulanic acid 16/8 \n", - "21 amoxicillin/clavulanic acid 16/8 \n", - "22 amoxicillin/clavulanic acid 16/8 \n", - "23 amoxicillin/clavulanic acid 16/8 \n", - "24 polymyxin B 1 \n", - "25 polymyxin B 1 \n", - "26 polymyxin B 8 \n", - "27 polymyxin B 4 " - ] - }, - "execution_count": 43, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# read user AST data with selected 3 columns\n", - "strain_mic=pd.read_csv(input_user, sep=',', usecols =['Strain name', 'Antibiotics', 'MIC'],na_filter=False)\n", - "#strain_mic" - ] - }, - { - "cell_type": "code", - "execution_count": 44, - "id": "0d30ddc3", - "metadata": {}, - "outputs": [], - "source": [ - "clsi_bp=pd.read_csv(input_clsi,sep=',')\n", - "\n", - "#clsi_bp[clsi_bp[['Antibiotics', 'Susceptible']].duplicated()].shape" - ] - }, - { - "cell_type": "code", - "execution_count": 45, - "id": "a818676d", - "metadata": {}, - "outputs": [], - "source": [ - "#clsi_bp\n", - "#strain_mic" - ] - }, - { - "cell_type": "code", - "execution_count": 46, - "id": "c6b4c59b", - "metadata": {}, - "outputs": [], - "source": [ - "# convert MIC to numbers sMIC, rMIC\n", - "clsi_bp['s_mic'] =clsi_bp[['Susceptible']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n", - "clsi_bp['r_mic'] =clsi_bp[['Resistant']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n", - "clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))" - ] - }, - { - "cell_type": "code", - "execution_count": 47, - "id": "d0171f94", - "metadata": {}, - "outputs": [], - "source": [ - "#clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))" - ] - }, - { - "cell_type": "code", - "execution_count": 48, - "id": "fe45b2dd", - "metadata": {}, - "outputs": [], - "source": [ - "# Read only numbers in MIC values\n", - "#try:\n", - "strain_mic['o_mic']=strain_mic[['MIC']].applymap(lambda x: (re.sub(r'[^0-9.\\/]','', x)))\n", - "#except TypeError:\n", - "# print('Waring: Error in MIC value')" - ] - }, - { - "cell_type": "code", - "execution_count": 49, - "id": "ddbbe4d9", - "metadata": {}, - "outputs": [], - "source": [ - "#strain_mic" - ] - }, - { - "cell_type": "code", - "execution_count": 50, - "id": "640508f1", - "metadata": {}, - "outputs": [], - "source": [ - "# capitalize each Antibiotic Name for comparision with removing whitespace\n", - "strain_mic['Strain name']=strain_mic['Strain name'].str.capitalize().str.replace(\" \",\"\")\n", - "strain_mic['Antibiotics']=strain_mic['Antibiotics'].str.capitalize().str.replace(\" \",\"\")\n", - "\n", - "clsi_bp['Antibiotics']=clsi_bp['Antibiotics'].str.capitalize().str.replace(\" \",\"\")" - ] - }, - { - "cell_type": "code", - "execution_count": 51, - "id": "b87426f4", - "metadata": {}, - "outputs": [], - "source": [ - "#find duplicate values in input files\n", - "dups=strain_mic[strain_mic[['Strain name', 'Antibiotics']].duplicated(keep=False)]\n", - "if dups.shape[0] != 0:\n", - " print ('Please provide a single MIC value in input file for given duplicates combination of \\'Strain name and Antibiotics\\' to use the tool:-\\n',dups)\n", - " #exit()\n", - "else:\n", - " #compare CLSI Antibiotics only\n", - " #result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner', indicator=True)[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','_merge']]\n", - " try:\n", - " result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner')[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','i_mic']]\n", - " except KeyError:\n", - " print('Waring: Error in input Values')" - ] - }, - { - "cell_type": "code", - "execution_count": 52, - "id": "91bfc94d", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "<div>\n", - "<style scoped>\n", - " .dataframe tbody tr th:only-of-type {\n", - " vertical-align: middle;\n", - " }\n", - "\n", - " .dataframe tbody tr th {\n", - " vertical-align: top;\n", - " }\n", - "\n", - " .dataframe thead th {\n", - " text-align: right;\n", - " }\n", - "</style>\n", - "<table border=\"1\" class=\"dataframe\">\n", - " <thead>\n", - " <tr style=\"text-align: right;\">\n", - " <th></th>\n", - " <th>Strain name</th>\n", - " <th>Antibiotics</th>\n", - " <th>MIC</th>\n", - " <th>o_mic</th>\n", - " <th>s_mic</th>\n", - " <th>r_mic</th>\n", - " <th>i_mic</th>\n", - " </tr>\n", - " </thead>\n", - " <tbody>\n", - " <tr>\n", - " <th>0</th>\n", - " <td>Acinetobacterbaumanniia85</td>\n", - " <td>Colistin</td>\n", - " <td>0.1</td>\n", - " <td>0.1</td>\n", - " <td>-</td>\n", - " <td>4</td>\n", - " <td>2</td>\n", - " </tr>\n", - " <tr>\n", - " <th>1</th>\n", - " <td>Acinetobacterbaumanniidu202</td>\n", - " <td>Colistin</td>\n", - " <td></td>\n", - " <td></td>\n", - " <td>-</td>\n", - " <td>4</td>\n", - " <td>2</td>\n", - " </tr>\n", - " <tr>\n", - " <th>2</th>\n", - " <td>Acinetobacterbaumanniia85</td>\n", - " <td>Netilmicin</td>\n", - " <td>1</td>\n", - " <td>1</td>\n", - " <td>8</td>\n", - " <td>32</td>\n", - " <td>16</td>\n", - " </tr>\n", - " <tr>\n", - " <th>3</th>\n", - " <td>Acinetobacterbaumanniiab307-0294</td>\n", - " <td>Ampicillin/sulbactam</td>\n", - " <td>mg/L</td>\n", - " <td>/</td>\n", - " <td>8/4</td>\n", - " <td>32/16</td>\n", - " <td>16/8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>4</th>\n", - " <td>Acinetobacterbaumanniidu202</td>\n", - " <td>Ampicillin/sulbactam</td>\n", - " <td>>=0.3 mg/L</td>\n", - " <td>0.3/</td>\n", - " <td>8/4</td>\n", - " <td>32/16</td>\n", - " <td>16/8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>5</th>\n", - " <td>Acinetobacterbaumanniiab307-0294</td>\n", - " <td>Piperacillin/tazobactam</td>\n", - " <td>0</td>\n", - " <td>0</td>\n", - " <td>16/4</td>\n", - " <td>128/4</td>\n", - " <td>32/4-64/4</td>\n", - " </tr>\n", - " <tr>\n", - " <th>6</th>\n", - " <td>Acinetobacterbaumanniidu202</td>\n", - " <td>Piperacillin/tazobactam</td>\n", - " <td>NA</td>\n", - " <td></td>\n", - " <td>16/4</td>\n", - " <td>128/4</td>\n", - " <td>32/4-64/4</td>\n", - " </tr>\n", - " <tr>\n", - " <th>7</th>\n", - " <td>Acinetobacterbaumanniiorab01</td>\n", - " <td>Piperacillin/tazobactam</td>\n", - " <td>>64/4</td>\n", - " <td>64/4</td>\n", - " <td>16/4</td>\n", - " <td>128/4</td>\n", - " <td>32/4-64/4</td>\n", - " </tr>\n", - " <tr>\n", - " <th>8</th>\n", - " <td>Acinetobacterbaumanniiab307-0294</td>\n", - " <td>Ceftriaxone</td>\n", - " <td>16</td>\n", - " <td>16</td>\n", - " <td>8</td>\n", - " <td>64</td>\n", - " <td>16-32</td>\n", - " </tr>\n", - " <tr>\n", - " <th>9</th>\n", - " <td>Acinetobacterbaumanniiab307-0294</td>\n", - " <td>Cefepime</td>\n", - " <td>8</td>\n", - " <td>8</td>\n", - " <td>8</td>\n", - " <td>32</td>\n", - " <td>16</td>\n", - " </tr>\n", - " <tr>\n", - " <th>10</th>\n", - " <td>Acinetobacterbaumanniiab5075-uw</td>\n", - " <td>Cefepime</td>\n", - " <td>>256</td>\n", - " <td>256</td>\n", - " <td>8</td>\n", - " <td>32</td>\n", - " <td>16</td>\n", - " </tr>\n", - " <tr>\n", - " <th>11</th>\n", - " <td>Acinetobacterbaumanniiab307-0294</td>\n", - " <td>Meropenem</td>\n", - " <td>0.25</td>\n", - " <td>0.25</td>\n", - " <td>2</td>\n", - " <td>8</td>\n", - " <td>4</td>\n", - " </tr>\n", - " <tr>\n", - " <th>12</th>\n", - " <td>Acinetobacterbaumanniiab307-0294</td>\n", - " <td>Imipenem</td>\n", - " <td>1</td>\n", - " <td>1</td>\n", - " <td>2</td>\n", - " <td>8</td>\n", - " <td>4</td>\n", - " </tr>\n", - " <tr>\n", - " <th>13</th>\n", - " <td>Acinetobacterbaumanniiab5075-uw</td>\n", - " <td>Ceftazidime</td>\n", - " <td>>128</td>\n", - " <td>128</td>\n", - " <td>8</td>\n", - " <td>32</td>\n", - " <td>16</td>\n", - " </tr>\n", - " <tr>\n", - " <th>14</th>\n", - " <td>Acinetobacterbaumanniiab5075-uw</td>\n", - " <td>Ciprofloxacin</td>\n", - " <td>>32</td>\n", - " <td>32</td>\n", - " <td>1</td>\n", - " <td>4</td>\n", - " <td>2</td>\n", - " </tr>\n", - " <tr>\n", - " <th>15</th>\n", - " <td>Acinetobacterbaumanniidu202</td>\n", - " <td>Ticarcillin/clavulanicacid</td>\n", - " <td>>=128/2</td>\n", - " <td>128/2</td>\n", - " <td>16/2</td>\n", - " <td>128/2</td>\n", - " <td>32/2-64/2</td>\n", - " </tr>\n", - " <tr>\n", - " <th>16</th>\n", - " <td>Acinetobacterbaumanniidu202</td>\n", - " <td>Trimethoprim/sulfamethoxazole</td>\n", - " <td>8/152</td>\n", - " <td>8/152</td>\n", - " <td>2/38</td>\n", - " <td>4/76</td>\n", - " <td>-</td>\n", - " </tr>\n", - " <tr>\n", - " <th>17</th>\n", - " <td>Acinetobacterbaumanniistrainfda-cdc-ar_0305</td>\n", - " <td>Polymyxinb</td>\n", - " <td>1</td>\n", - " <td>1</td>\n", - " <td>-</td>\n", - " <td>4</td>\n", - " <td>2</td>\n", - " </tr>\n", - " <tr>\n", - " <th>18</th>\n", - " <td>Acinetobacterbaumanniistrainfda-cdc-ar_0306</td>\n", - " <td>Polymyxinb</td>\n", - " <td>1</td>\n", - " <td>1</td>\n", - " <td>-</td>\n", - " <td>4</td>\n", - " <td>2</td>\n", - " </tr>\n", - " <tr>\n", - " <th>19</th>\n", - " <td>Acinetobacterbaumanniistrainfda-cdc-ar_0307</td>\n", - " <td>Polymyxinb</td>\n", - " <td>8</td>\n", - " <td>8</td>\n", - " <td>-</td>\n", - " <td>4</td>\n", - " <td>2</td>\n", - " </tr>\n", - " <tr>\n", - " <th>20</th>\n", - " <td>Acinetobacterbaumanniistrainfda-cdc-ar_0308</td>\n", - " <td>Polymyxinb</td>\n", - " <td>4</td>\n", - " <td>4</td>\n", - " <td>-</td>\n", - " <td>4</td>\n", - " <td>2</td>\n", - " </tr>\n", - " </tbody>\n", - "</table>\n", - "</div>" - ], - "text/plain": [ - " Strain name \\\n", - "0 Acinetobacterbaumanniia85 \n", - "1 Acinetobacterbaumanniidu202 \n", - "2 Acinetobacterbaumanniia85 \n", - "3 Acinetobacterbaumanniiab307-0294 \n", - "4 Acinetobacterbaumanniidu202 \n", - "5 Acinetobacterbaumanniiab307-0294 \n", - "6 Acinetobacterbaumanniidu202 \n", - "7 Acinetobacterbaumanniiorab01 \n", - "8 Acinetobacterbaumanniiab307-0294 \n", - "9 Acinetobacterbaumanniiab307-0294 \n", - "10 Acinetobacterbaumanniiab5075-uw \n", - "11 Acinetobacterbaumanniiab307-0294 \n", - "12 Acinetobacterbaumanniiab307-0294 \n", - "13 Acinetobacterbaumanniiab5075-uw \n", - "14 Acinetobacterbaumanniiab5075-uw \n", - "15 Acinetobacterbaumanniidu202 \n", - "16 Acinetobacterbaumanniidu202 \n", - "17 Acinetobacterbaumanniistrainfda-cdc-ar_0305 \n", - "18 Acinetobacterbaumanniistrainfda-cdc-ar_0306 \n", - "19 Acinetobacterbaumanniistrainfda-cdc-ar_0307 \n", - "20 Acinetobacterbaumanniistrainfda-cdc-ar_0308 \n", - "\n", - " Antibiotics MIC o_mic s_mic r_mic i_mic \n", - "0 Colistin 0.1 0.1 - 4 2 \n", - "1 Colistin - 4 2 \n", - "2 Netilmicin 1 1 8 32 16 \n", - "3 Ampicillin/sulbactam mg/L / 8/4 32/16 16/8 \n", - "4 Ampicillin/sulbactam >=0.3 mg/L 0.3/ 8/4 32/16 16/8 \n", - "5 Piperacillin/tazobactam 0 0 16/4 128/4 32/4-64/4 \n", - "6 Piperacillin/tazobactam NA 16/4 128/4 32/4-64/4 \n", - "7 Piperacillin/tazobactam >64/4 64/4 16/4 128/4 32/4-64/4 \n", - "8 Ceftriaxone 16 16 8 64 16-32 \n", - "9 Cefepime 8 8 8 32 16 \n", - "10 Cefepime >256 256 8 32 16 \n", - "11 Meropenem 0.25 0.25 2 8 4 \n", - "12 Imipenem 1 1 2 8 4 \n", - "13 Ceftazidime >128 128 8 32 16 \n", - "14 Ciprofloxacin >32 32 1 4 2 \n", - "15 Ticarcillin/clavulanicacid >=128/2 128/2 16/2 128/2 32/2-64/2 \n", - "16 Trimethoprim/sulfamethoxazole 8/152 8/152 2/38 4/76 - \n", - "17 Polymyxinb 1 1 - 4 2 \n", - "18 Polymyxinb 1 1 - 4 2 \n", - "19 Polymyxinb 8 8 - 4 2 \n", - "20 Polymyxinb 4 4 - 4 2 " - ] - }, - "execution_count": 52, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#result" - ] - }, - { - "cell_type": "code", - "execution_count": 53, - "id": "b171f205", - "metadata": {}, - "outputs": [], - "source": [ - "#compare MIC values and assign Susceptible and Resistant to Strain\n", - "#try:\n", - "result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res_int,axis = 1)\n", - "#except ValueError:\n", - "# print('Waring: Error in input MIC value')" - ] - }, - { - "cell_type": "code", - "execution_count": 54, - "id": "3336fd92", - "metadata": {}, - "outputs": [], - "source": [ - "#result" - ] - }, - { - "cell_type": "code", - "execution_count": 55, - "id": "f0dacfd1", - "metadata": {}, - "outputs": [], - "source": [ - "#result[['Strain name', 'Antibiotics', 'MIC','s_mic','r_mic','CLSI_profile']].to_csv(output_profile,sep=',', index=False, encoding='utf-8-sig')" - ] - }, - { - "cell_type": "code", - "execution_count": 56, - "id": "3d8d03f7", - "metadata": {}, - "outputs": [], - "source": [ - "#create a pivot table for ASIST\n", - "table=result[['Strain name', 'Antibiotics','CLSI_profile']].drop_duplicates()\n", - "result_table=pd.pivot_table(table, values ='CLSI_profile', index =['Strain name'],columns =['Antibiotics'], aggfunc = lambda x: ' '.join(x))" - ] - }, - { - "cell_type": "code", - "execution_count": 57, - "id": "7d7223a3", - "metadata": {}, - "outputs": [], - "source": [ - "#result_table" - ] - }, - { - "cell_type": "code", - "execution_count": 58, - "id": "8a41b2ef", - "metadata": {}, - "outputs": [], - "source": [ - "#result_table.to_csv(output_table,na_rep='NA')" - ] - }, - { - "cell_type": "code", - "execution_count": 59, - "id": "8c9e5f87", - "metadata": {}, - "outputs": [], - "source": [ - "# reorder the Antibiotics for ASIST\n", - "clsi_ab=['Amikacin','Tobramycin','Gentamycin','Netilmicin','Imipenem','Meropenem','Doripenem','Ciprofloxacin','Levofloxacin',\n", - " 'Piperacillin/tazobactam','Ticarcillin/clavulanicacid','Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime',\n", - " 'Trimethoprim/sulfamethoxazole','Ampicillin/sulbactam','Colistin','Polymyxinb','Tetracycline','Doxicycline ',\n", - " 'Minocycline']\n", - "result_selected=result_table.filter(clsi_ab)" - ] - }, - { - "cell_type": "code", - "execution_count": 60, - "id": "cdf43afb", - "metadata": {}, - "outputs": [], - "source": [ - "#print(result_selected.shape, result_table.shape)" - ] - }, - { - "cell_type": "code", - "execution_count": 61, - "id": "c4c4df30", - "metadata": {}, - "outputs": [], - "source": [ - "#result_selected.insert(0,'Resistance_phenotype','')" - ] - }, - { - "cell_type": "code", - "execution_count": 62, - "id": "9adb2703", - "metadata": {}, - "outputs": [], - "source": [ - "#rename headers\n", - "result_selected=result_selected.rename(columns = {'Ticarcillin/clavulanicacid':'Ticarcillin/clavulanic acid','Piperacillin/tazobactam':'Piperacillin/ tazobactam','Trimethoprim/sulfamethoxazole': 'Trimethoprim/ sulfamethoxazole','Ampicillin/sulbactam':'Ampicillin/ sulbactam', 'Polymyxinb': 'Polymyxin B'} )" - ] - }, - { - "cell_type": "code", - "execution_count": 63, - "id": "50e6cf5f", - "metadata": {}, - "outputs": [], - "source": [ - "#result_selected" - ] - }, - { - "cell_type": "code", - "execution_count": 64, - "id": "2833671c", - "metadata": {}, - "outputs": [], - "source": [ - "result_selected.to_csv(output_table,na_rep='NA')" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -}
--- a/input.csv_table.csv Mon Jun 28 15:05:17 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/clavulanic acid,Ceftriaxone,Ceftazidime,Cefepime,Trimethoprim/ sulfamethoxazole,Ampicillin/ sulbactam,Colistin,Polymyxin B -Acinetobacter baumannii A85,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Strain could not be classified Intermediate,NA -Acinetobacter baumannii AB307-0294,,Susceptible,Susceptible,NA,Strain could not be classified,NA,Intermediate,NA,Susceptible,NA,Strain could not be 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 be classified,Resistant,NA,NA,NA,Resistant,Strain could not be classified,Strain could not be 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,Strain could not be classified -Acinetobacter baumannii strain FDA-CDC-AR_0306,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Strain could not be classified -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/output.csv Mon Jun 28 15:05:17 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/suite_config.xml Mon Jun 28 15:05:17 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<suite id='suite_asist_tools' name='Suite of ASIST tools' version="1.0.0"> - <description>This suite contains clsi_profile and asist files and wrappers for Galaxy</description> - <tool id="clsi_profile" name="CLSI Profile" version="0.1.6" python_template_version="3.5"> - <description>MIC profile using CLSI MIC breakpoints</description> - </tool> - <tool id="asist" name="ASIST" version="1.0.1" python_template_version="3.5"> - <description>Antimicrobial Susceptibility standards based phenotypes</description> - </tool> -</suite>
--- a/tool.sh Mon Jun 28 15:05:17 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -#!/bin/bash - -planemo tool_init --id 'clsi_profile' --name 'CLSI Profile' \ - --description 'MIC profile using CLSI MIC breakpoints' \ - --requirement 'python' \ - --example_command "clsi_profile_type2.py 'input.csv' 'clsi.csv' 'output.csv'" \ - --example_input input.csv \ - --example_input clsi.csv \ - --example_output output.csv \ - --test_case \ -# --version_command 'python3 -V' \ -# --help_from_command '' \ -# --doi '' - -planemo lint