# HG changeset patch
# User rakesh4osdd
# Date 1624692473 0
# Node ID c1a77856070c25cfe59fb74aa1ce90fe18f5c69c

"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"

diff -r 000000000000 -r c1a77856070c LICENSE
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,21 @@
+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.
diff -r 000000000000 -r c1a77856070c README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,20 @@
+# clsi_profile
+
+ 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**
+
+ 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).
+
+**Example Input CSV file:**
+
+	Strain name,Resistance_phenotype,Antibiotic_A1,Antibiotic_A2,Antibiotic_A_N
+	Strain_1,Phenotype_1,Resistant,Resistant,Resistant
+	Strain_2,Phenotype_2,Resistant,Susceptible,Resistant
+
+ Link to the code : https://github.com/rakesh4osdd/asist
+ 
+ 
+# ASIST tool suite
+
+ These tools can be install from Galaxy toolshed to a Galaxy installation https://galaxyproject.org/admin/get-galaxy/.
diff -r 000000000000 -r c1a77856070c asist.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/asist.xml	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,48 @@
+<tool id="asist" name="ASIST" version="1.0.1" python_template_version="3.5">
+    <description>Antimicrobial Susceptibility standards based phenotypes</description>
+    <requirements>
+        <requirement type="package">pandas</requirement>
+    </requirements>
+    <version_command>python -c "import pandas; print(pandas.__version__)"</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+	    "${__tool_directory__}/asist_dynamic.py" "$input1" "$output1"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="csv" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="csv" from_work_dir="test-data/asist_output.csv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="test-data/asist_input.csv"/>
+            <output name="output1" file="test-data/asist_output.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Input CSV file example:
+	    Strain name,Amikacin,Tobramycin,Gentamycin,Imipenem
+	    Strain name,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems
+	    Acinetobacter baumannii strain FDA-CDC-AR_0288,Resistant,Resistant,Resistant,Resistant
+	    Acinetobacter baumannii strain FDA-CDC-AR_0303,Resistant,Resistant,Resistant,Resistant
+	    Acinetobacter baumannii strain FDA-CDC-AR_0304,NA,Resistant,Resistant,Resistant
+	Output CSV file example:
+	    Strain name,Strain phenotype,Amikacin,Tobramycin,Gentamycin,Imipenem
+	    Strain name,Strain could not be classified,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems
+	    Acinetobacter baumannii strain FDA-CDC-AR_0288,Strain could not be classified,Resistant,Resistant,Resistant,Resistant
+	    Acinetobacter baumannii strain FDA-CDC-AR_0303,Strain could not be classified,Resistant,Resistant,Resistant,Resistant
+	    Acinetobacter baumannii strain FDA-CDC-AR_0304,Strain could not be classified,NA,Resistant,Resistant,Resistant
+    ]]></help>
+    <citations>
+	    <citation type="bibtex">@ARTICLE{Sharma_2021,
+		    	author = {Tina Sharma and Rakesh Kumar and Anshu Bhardwaj},
+		    	title = {ASIST: Antimicrobial Susceptibility standards based phenotypes},
+		    	journal = {},
+		        year = {2021},
+		    	volume = {},
+		    	pages = {},
+		    	url = {https://ab-openlab.csir.res.in/asist}
+		    }
+	    </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r c1a77856070c asist_dynamic.ipynb
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/asist_dynamic.ipynb	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,310 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1309,
+   "id": "27cfc66f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#ASIST program for phenotype based on Antibiotics profile\n",
+    "# create a profile based on selected antibiotics only\n",
+    "# rakesh4osdd@gmail.com, 14-June-2021"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "75a352b7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "import sys\n",
+    "import os\n",
+    "from collections import Counter"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 176,
+   "id": "d66ec0d2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "input_file=sys.argv[1]\n",
+    "output_file=sys.argv[2]\n",
+    "#input_file='test-data/asist_input.csv'\n",
+    "#output_file='test-data/asist_output.csv'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 177,
+   "id": "bf24c946",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# strain_profile to phenotype condition\n",
+    "def s_phen(sus,res,intm,na,pb_sus):\n",
+    "    if (sus>0 and res==0 and na>=0):\n",
+    "        #print('Possible Susceptible')\n",
+    "        phen='Possible Susceptible'\n",
+    "    elif (sus>=0 and 3<=res<7 and na>=0 and pb_sus==0):\n",
+    "        #print('Possible MDR')\n",
+    "        phen='Possible MDR'\n",
+    "    elif (sus>=0 and 7<=res<9 and na>=0 and pb_sus==0):\n",
+    "        #print('Possible XDR')\n",
+    "        phen='Possible XDR'\n",
+    "    #special cases\n",
+    "    elif (sus>=1 and res>0 and na>=0 and pb_sus==1):\n",
+    "        #print('Possible XDR')\n",
+    "        phen='Possible XDR'\n",
+    "    #special cases\n",
+    "    elif (sus>0 and res==9 and na>=0):\n",
+    "        #print('Possible XDR')\n",
+    "        phen='Possible XDR'\n",
+    "    elif (sus==0 and res==9 and na>=0):\n",
+    "        #print('Possible TDR')\n",
+    "        phen='Possible TDR'\n",
+    "    else:\n",
+    "        #print('Strain could not be classified')\n",
+    "        phen='Strain could not be classified ('+ str(intm)+' | ' + str(na) +')'\n",
+    "    return(phen)\n",
+    "\n",
+    "#print(s_phen(1,9,0,0))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 178,
+   "id": "8bad7d9d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# define Antibiotic groups as per antibiotic of CLSI breakpoints MIC\n",
+    "#Aminoglycoside\n",
+    "cat1=['Amikacin','Tobramycin','Gentamycin','Netilmicin']\n",
+    "#Beta-lactams- Carbapenems\n",
+    "cat2=['Imipenem','Meropenam','Doripenem']\n",
+    "#Fluoroquinolone\n",
+    "cat3=['Ciprofloxacin','Levofloxacin']\n",
+    "#Beta-lactam inhibitor\n",
+    "cat4=['Piperacillin/tazobactam','Ticarcillin/clavulanicacid']\n",
+    "#Cephalosporin\n",
+    "cat5=['Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime']\n",
+    "#Sulfonamides\n",
+    "cat6=['Trimethoprim/sulfamethoxazole']\n",
+    "#Penicillins/beta-lactamase\n",
+    "cat7=['Ampicillin/sulbactam']\n",
+    "#Polymyxins\n",
+    "cat8=['Colistin','Polymyxinb']\n",
+    "#Tetracycline\n",
+    "cat9=['Tetracycline','Doxicycline','Minocycline']\n",
+    "\n",
+    "def s_profiler(pd_series):\n",
+    "    #print(type(pd_series),'\\n', pd_series)\n",
+    "    #create a dictionary of dataframe series\n",
+    "    cats={'s1':cat1,'s2':cat2,'s3':cat3,'s4':cat4,'s5':cat5,'s6':cat6,'s7':cat7,'s8':cat8,'s9':cat9}\n",
+    "    # find the antibiotics name in input series\n",
+    "    for cat in cats:\n",
+    "        #print(cats[cat])\n",
+    "        cats[cat]=pd_series.filter(cats[cat])\n",
+    "        #print(cats[cat])\n",
+    "    #define res,sus,intm,na,pb_sus\n",
+    "    res=0\n",
+    "    sus=0\n",
+    "    intm=0\n",
+    "    na=0\n",
+    "    pb_sus=0\n",
+    "    # special case of 'Polymyxin b' for its value\n",
+    "    if 'Polymyxinb' in pd_series:\n",
+    "        ctp=cats['s8']['Polymyxinb'].strip().lower()\n",
+    "        if ctp == 'susceptible':\n",
+    "            pb_sus=1\n",
+    "        #print((ctp,p_sus))\n",
+    "    # check all categories\n",
+    "    for cat in cats:\n",
+    "        #ctp=cats['s8'].iloc[i:i+1].stack().value_counts().to_dict()\n",
+    "        #print(ctp)\n",
+    "        # Pandas series\n",
+    "        ct=cats[cat].value_counts().to_dict()\n",
+    "        #print(ct)\n",
+    "        # remove whitespace and convert to lowercase words\n",
+    "        ct =  {k.strip().lower(): v for k, v in ct.items()}\n",
+    "        #print(ct)\n",
+    "        k=Counter(ct)\n",
+    "        #j=Counter(ct)+Counter(j)\n",
+    "        #print(j)\n",
+    "        # category wise marking\n",
+    "        if k['resistant']>=1:\n",
+    "            res=res+1\n",
+    "        if k['susceptible']>=1:\n",
+    "            sus=sus+1\n",
+    "        if k['intermediate']>=1:\n",
+    "            intm=intm+1\n",
+    "        if k['na']>=1:\n",
+    "            na=na+1\n",
+    "    #print(sus,res,intm,na,pb_sus)\n",
+    "    #print(s_phen(sus,res,intm,na,pb_sus))\n",
+    "    return(s_phen(sus,res,intm,na,pb_sus))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 179,
+   "id": "7629fc10",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#input_file='input2.csv_table.csv'\n",
+    "#output_file=input_file+'_output.txt'\n",
+    "strain_profile=pd.read_csv(input_file, sep=',',na_filter=False,skipinitialspace = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 180,
+   "id": "bed1abba",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "old_strain_name=strain_profile.columns[0]\n",
+    "new_strain_name=old_strain_name.capitalize().strip().replace(' ', '')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 181,
+   "id": "a64b5022",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# make header capitalization, remove leading,lagging, and multiple whitespace for comparision\n",
+    "strain_profile.columns=strain_profile.columns.str.capitalize().str.strip().str.replace('\\s+', '', regex=True)\n",
+    "#print(strain_profile.columns)\n",
+    "#strain_profile.head()\n",
+    "#strain_profile.columns"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 182,
+   "id": "caac57d7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# add new column in dataframe on second position\n",
+    "strain_profile.insert(1, 'Strain phenotype','')\n",
+    "#strain_profile.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 183,
+   "id": "eb4b0c4d",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "strain_profile['Strain phenotype'] = strain_profile.apply(lambda x: (s_profiler(x)), axis=1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 184,
+   "id": "86441c0f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#strain_profile.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 185,
+   "id": "75698be5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#rename headers for old name\n",
+    "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'} )"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 186,
+   "id": "c14a13eb",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "#strain_profile.columns"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 187,
+   "id": "ff484767",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#strain_profile"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 188,
+   "id": "5ab72211",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "strain_profile.to_csv(output_file,na_rep='NA',index=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 189,
+   "id": "020dbe85",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Open a file with access mode 'a'\n",
+    "with open(output_file, \"a\") as file_object:\n",
+    "    # Append 'hello' at the end of file\n",
+    "    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')\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9c17e66a",
+   "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": "3.7.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff -r 000000000000 -r c1a77856070c asist_dynamic.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/asist_dynamic.py	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,190 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# In[1309]:
+
+
+#ASIST program for phenotype based on Antibiotics profile
+# create a profile based on selected antibiotics only
+# rakesh4osdd@gmail.com, 14-June-2021
+
+
+# In[1403]:
+
+
+import pandas as pd
+import sys
+import os
+from collections import Counter
+
+
+# In[ ]:
+
+
+input_file=sys.argv[1]
+output_file=sys.argv[2]
+
+
+# In[1362]:
+
+
+# strain_profile to phenotype condition
+def s_phen(sus,res,na,pb_sus):
+    if (sus>0 and res==0 and na>=0):
+        #print('Possible Susceptible')
+        phen='Possible Susceptible'
+    elif (sus>=0 and 3<=res<7 and na>=0 and pb_sus==0):
+        #print('Possible MDR')
+        phen='Possible MDR'
+    elif (sus>=0 and 7<=res<9 and na>=0 and pb_sus==0):
+        #print('Possible XDR')
+        phen='Possible XDR'
+    #special cases
+    elif (sus>=1 and res>0 and na>=0 and pb_sus==1):
+        #print('Possible XDR')
+        phen='Possible XDR'
+    #special cases
+    elif (sus>0 and res==9 and na>=0):
+        #print('Possible XDR')
+        phen='Possible XDR'
+    elif (sus==0 and res==9 and na>=0):
+        #print('Possible TDR')
+        phen='Possible TDR'
+    else:
+        #print('Strain could not be classified')
+        phen='Strain could not be classified'
+    return(phen)
+
+#print(s_phen(1,9,0,0))
+
+
+# In[1363]:
+
+
+# define Antibiotic groups as per antibiotic of CLSI breakpoints MIC
+#Aminoglycoside
+cat1=['Amikacin','Tobramycin','Gentamycin','Netilmicin']
+#Beta-lactams- Carbapenems
+cat2=['Imipenem','Meropenam','Doripenem']
+#Fluoroquinolone
+cat3=['Ciprofloxacin','Levofloxacin']
+#Beta-lactam inhibitor
+cat4=['Piperacillin/tazobactam','Ticarcillin/clavulanicacid']
+#Cephalosporin
+cat5=['Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime']
+#Sulfonamides
+cat6=['Trimethoprim/sulfamethoxazole']
+#Penicillins/beta-lactamase
+cat7=['Ampicillin/sulbactam']
+#Polymyxins
+cat8=['Colistin','Polymyxinb']
+#Tetracycline
+cat9=['Tetracycline','Doxicycline','Minocycline']
+
+def s_profiler(pd_series):
+    #print(type(pd_series),'\n', pd_series)
+    #create a dictionary of dataframe series
+    cats={'s1':cat1,'s2':cat2,'s3':cat3,'s4':cat4,'s5':cat5,'s6':cat6,'s7':cat7,'s8':cat8,'s9':cat9}
+    # find the antibiotics name in input series
+    for cat in cats:
+        #print(cats[cat])
+        cats[cat]=pd_series.filter(cats[cat])
+        #print(cats[cat])
+    #define res,sus,na,pb_sus
+    res=0
+    sus=0
+    na=0
+    pb_sus=0
+    # special case of 'Polymyxin b' for its value
+    if 'Polymyxinb' in pd_series:
+        ctp=cats['s8']['Polymyxinb'].strip().lower()
+        if ctp == 'susceptible':
+            pb_sus=1
+        #print((ctp,p_sus))
+    # check all categories
+    for cat in cats:
+        #ctp=cats['s8'].iloc[i:i+1].stack().value_counts().to_dict()
+        #print(ctp)
+        # Pandas series
+        ct=cats[cat].value_counts().to_dict()
+        #print(ct)
+        # remove whitespace and convert to lowercase words
+        ct =  {k.strip().lower(): v for k, v in ct.items()}
+        #print(ct)
+        k=Counter(ct)
+        #j=Counter(ct)+Counter(j)
+        #print(j)
+        # category wise marking
+        if k['resistant']>=1:
+            res=res+1
+        if k['susceptible']>=1:
+            sus=sus+1
+        if k['na']>=1:
+            na=na+1
+    #print(s_phen(sus,res,na,pb_sus))
+    return(s_phen(sus,res,na,pb_sus))
+
+
+# In[1397]:
+
+
+#input_file='input2.csv_table.csv'
+#output_file=input_file+'_output.txt'
+strain_profile=pd.read_csv(input_file, sep=',',na_filter=False,skipinitialspace = True)
+
+
+# In[1387]:
+
+
+old_strain_name=strain_profile.columns[0]
+new_strain_name=old_strain_name.capitalize().strip().replace(' ', '')
+
+
+# In[1388]:
+
+
+# make header capitalization, remove leading,lagging, and multiple whitespace for comparision
+strain_profile.columns=strain_profile.columns.str.capitalize().str.strip().str.replace('\s+', '', regex=True)
+#print(strain_profile.columns)
+#strain_profile.head()
+#strain_profile.columns
+
+
+# In[1389]:
+
+
+# add new column in dataframe on second position
+strain_profile.insert(1, 'Strain phenotype','')
+#strain_profile.head()
+
+
+# In[1390]:
+
+
+strain_profile['Strain phenotype'] = strain_profile.apply(lambda x: (s_profiler(x)), axis=1)
+
+
+# In[1391]:
+
+
+#strain_profile.head()
+
+
+# In[1392]:
+
+
+#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]:
+
+
+#strain_profile
+
+
+# In[1394]:
+
+
+strain_profile.to_csv(output_file,na_rep='NA',index=False)
+
diff -r 000000000000 -r c1a77856070c clsi.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clsi.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,23 @@
+Antibiotics,Susceptible,Resistant,Intermediate
+Amikacin,≤ 16,≥ 64,32
+Tobramycin,≤ 4,≥ 16,8
+Gentamicin,≤ 4,≥ 16,8
+Netilmicin,≤ 8,≥ 32,16
+Imipenem,≤ 2,≥ 8,4
+Meropenem,≤ 2,≥ 8,4
+Doripenem,≤ 2,≥ 8,4
+Ciprofloxacin,≤ 1,≥ 4,2
+Levofloxacin,≤ 2,≥ 8,4
+Piperacillin/ tazobactam,≤ 16/4,≥ 128/4,32/4-64/4
+Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2,32/2-64/2
+Cefotaxime,≤ 8,≥ 64,16-32
+Ceftriaxone,≤ 8,≥ 64,16-32
+Ceftazidime,≤ 8,≥ 32,16
+Cefepime,≤ 8,≥ 32,16
+Trimethoprim/ sulfamethoxazole,≤ 2/38,≥ 4/76,-
+Ampicillin/ sulbactam,≤ 8/4,≥ 32/16,16/8
+Colistin,-,≥ 4,≤ 2
+Polymyxin B,-,≥ 4,≤ 2
+Tetracycline,≤ 4,≥ 16,8
+Doxycycline,≤ 4,≥ 16,8
+Minocycline,≤ 4,≥ 16,8
\ No newline at end of file
diff -r 000000000000 -r c1a77856070c clsi_profile.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clsi_profile.py	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,305 @@
+#!/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')
+
diff -r 000000000000 -r c1a77856070c clsi_profile_type2.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clsi_profile_type2.py	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,244 @@
+#!/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[ ]:
+
+
+
+
diff -r 000000000000 -r c1a77856070c clsi_profile_type2_linux-Copy1.ipynb
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clsi_profile_type2_linux-Copy1.ipynb	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,2461 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "967b1345",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics\n",
+    "# By rakesh4osdd@gmail.com, 06-Jun-2021\n",
+    "import pandas as pd\n",
+    "import re\n",
+    "import sys"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "39e25c15",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "1.2.4 2.2.1\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(pd.__version__, re.__version__)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 175,
+   "id": "c96d7c62",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# cross check MIC values\n",
+    "def sus_res(mic):\n",
+    "    print(mic)\n",
+    "    #print ((mic,pd.isna(mic[1]),pd.isna(mic[0]),'\\n')\n",
+    "    if not (pd.isna(mic[0]) or pd.isna(mic[1]) or pd.isna(mic[2])):#check for NaN value\n",
+    "        #remove unwanted whitespace\n",
+    "        o_mic = mic[0].replace(' ', '')\n",
+    "        s_mic = mic[1].replace(' ', '')\n",
+    "        r_mic = mic[2].replace(' ', '')\n",
+    "        i_mic = mic[3].replace(' ', '')\n",
+    "        print(imic(o_mic,i_mic))\n",
+    "        #print (o_mic,s_mic,r_mic)\n",
+    "        #print (type(o_mic),type(s_mic),type(r_mic))\n",
+    "        if '/' in s_mic: #check for combination antibiotics\n",
+    "            #print ('combination antibiotics')\n",
+    "            try:\n",
+    "                if '/' in o_mic:\n",
+    "                    #print ('input combination')\n",
+    "                    if (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(o_mic.split('/')[1]) <= float(s_mic.split('/')[1])):\n",
+    "                        strain_type='Susceptible'\n",
+    "                    elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(o_mic.split('/')[1]) >= float(r_mic.split('/')[1])):\n",
+    "                        strain_type='Resistant'\n",
+    "                    elif (imic(o_mic,i_mic)):\n",
+    "                        strain_type='Intermediate-1'                    \n",
+    "                    else:\n",
+    "                        strain_type='Intermediate-2'\n",
+    "                else: \n",
+    "                    #print ('single')\n",
+    "                    if float(o_mic)==0:\n",
+    "                        strain_type='Strain could not classified'\n",
+    "                    elif (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(1) <= float(s_mic.split('/')[1])):\n",
+    "                        strain_type='Susceptible'\n",
+    "                    elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(1) >= float(r_mic.split('/')[1])):\n",
+    "                        strain_type='Resistant'\n",
+    "                    else:\n",
+    "                        strain_type='Intermediate-3'\n",
+    "            except ValueError:\n",
+    "                strain_type='Strain could not classified-1'\n",
+    "        elif (s_mic == '-'):\n",
+    "            if o_mic:\n",
+    "                if float(o_mic)==0:\n",
+    "                    strain_type='Strain could not classified-2'\n",
+    "                #elif (float(o_mic) <= float(s_mic)):\n",
+    "                #    strain_type='Susceptible'\n",
+    "                elif (float(o_mic) >= float(r_mic)):\n",
+    "                    strain_type='Resistant'\n",
+    "                elif (imic(o_mic,i_mic)):\n",
+    "                    strain_type='Intermediat-4'\n",
+    "                else:\n",
+    "                    strain_type='Intermediate-5'\n",
+    "            else:\n",
+    "                strain_type='Strain could not classified-3'\n",
+    "        else: #single antibiotics\n",
+    "            #print('single antibiotics')\n",
+    "            if o_mic:\n",
+    "                if float(o_mic)==0:\n",
+    "                    strain_type='Strain could not classified-4'\n",
+    "                elif (float(o_mic) <= float(s_mic)):\n",
+    "                    strain_type='Susceptible'\n",
+    "                elif (float(o_mic) >= float(r_mic)):\n",
+    "                    strain_type='Resistant'\n",
+    "                else:\n",
+    "                    strain_type='Intermediate-6'\n",
+    "            else:\n",
+    "                strain_type='Strain could not classified-5'\n",
+    "    else:\n",
+    "        strain_type='Strain could not classified-6'\n",
+    "    return(strain_type)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 176,
+   "id": "dbc70e34",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['32/2', '16/4', '128/4', '32/4-64/4']\n",
+      "32/2 32/4-64/4\n",
+      "False\n",
+      "32/2 32/4-64/4\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "'Intermediate-2'"
+      ]
+     },
+     "execution_count": 176,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mic=['32/2','16/4','128/4','32/4-64/4']\n",
+    "sus_res(mic)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "653b096e",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 202,
+   "id": "626a1e3f",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "65/4 64/4 s\n",
+      "65 4 64 4 s\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "'Strain could not classified-5'"
+      ]
+     },
+     "execution_count": 202,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "def check_mic(mic1,mic2,mic_type):\n",
+    "    print(mic1,mic2,mic_type)\n",
+    "    m1a = mic1.split('/')[0]\n",
+    "    m1b = mic1.split('/')[1]\n",
+    "    if '-' in mic2:   # for intermediate only\n",
+    "        m2a = mic2.split('-')[0].split('/')[0]\n",
+    "        m2b = mic2.split('-')[0].split('/')[1]\n",
+    "        m2aa = mic2.split('-')[1].split('/')[0]\n",
+    "        m2bb = mic2.split('-')[1].split('/')[1]\n",
+    "        if (float(m2aa)>=float(m1a)>=float(m2a) and float(m2b)>=float(m1b)>=float(m2b)):\n",
+    "            #print('intermediate')\n",
+    "            mic_type='Intermediate-1'\n",
+    "        else:\n",
+    "            #print('not define')\n",
+    "            mic_type='Strain could not classified-1'\n",
+    "        #print (m1a,m1b,m2a,m2b,m2aa,m2bb)\n",
+    "    else:\n",
+    "        m2a = mic2.split('/')[0]\n",
+    "        m2b = mic2.split('/')[1]\n",
+    "        print(m1a,m1b,m2a,m2b,mic_type)\n",
+    "        if mic_type=='s':\n",
+    "            if (float(m1a)<=float(m2a) and float(m1b)<=float(m2b)):\n",
+    "                mic_type='Susceptible'\n",
+    "            else:\n",
+    "                mic_type='Strain could not classified-5'\n",
+    "        elif mic_type=='r':\n",
+    "            if (float(m1a)>=float(m2a) and float(m1b)>=float(m2b)):\n",
+    "                mic_type='Resistant'\n",
+    "            else:\n",
+    "                mic_type='Strain could not classified-4'\n",
+    "        elif mic_type=='i':\n",
+    "            if (float(m1a)==float(m2a) and float(m1b)==float(m2b)):\n",
+    "                mic_type='Intermediate-2'\n",
+    "            else:\n",
+    "                mic_type='Strain could not classified-3'\n",
+    "        else:\n",
+    "            mic_type='Strain could not classified-2'\n",
+    "    return(mic_type)\n",
+    "        \n",
+    "check_mic('65/4','64/4','s')\n",
+    "#    float(mic1.split('/')[0]) <= float(mic2.split('/')[0]) and float(mic1.split('/')[1]) <= float(mic2.split('/')[1])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 171,
+   "id": "19905924",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#compare MIC values and assign Susceptible and Resistant to Strain\n",
+    "#try:\n",
+    "#result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res,axis = 1)\n",
+    "#except ValueError:\n",
+    "#    print('Waring: Error in input MIC value')\n",
+    "#result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res,axis = 1)\n",
+    "#del result['CLSI_profile']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 42,
+   "id": "7784b77d",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'input_user = sys.argv[1]\\ninput_clsi = sys.argv[2]\\noutput_table = sys.argv[3]'"
+      ]
+     },
+     "execution_count": 42,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# for input argument\n",
+    "\"\"\"input_user = sys.argv[1]\n",
+    "input_clsi = sys.argv[2]\n",
+    "output_table = sys.argv[3]\"\"\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 43,
+   "id": "1dee9127",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "input_user='input.csv'\n",
+    "input_clsi='clsi.csv'\n",
+    "output_profile=input_user+'_profile.csv'\n",
+    "output_table=input_user+'_table.csv'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "14c5cfd3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# read user AST data with selected 3 columns\n",
+    "strain_mic=pd.read_csv(input_user, sep=',', usecols =['Strain name', 'Antibiotics', 'MIC'],na_filter=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "77135cb7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "clsi_bp=pd.read_csv(input_clsi,sep=',')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "2ec1cbec",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Antibiotics</th>\n",
+       "      <th>Susceptible</th>\n",
+       "      <th>Resistant</th>\n",
+       "      <th>Intermediate</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>Amikacin</td>\n",
+       "      <td>≤ 16</td>\n",
+       "      <td>≥ 64</td>\n",
+       "      <td>32</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>Tobramycin</td>\n",
+       "      <td>≤ 4</td>\n",
+       "      <td>≥ 16</td>\n",
+       "      <td>8</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>Gentamicin</td>\n",
+       "      <td>≤ 4</td>\n",
+       "      <td>≥ 16</td>\n",
+       "      <td>8</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>Netilmicin</td>\n",
+       "      <td>≤ 8</td>\n",
+       "      <td>≥ 32</td>\n",
+       "      <td>16</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>Imipenem</td>\n",
+       "      <td>≤ 2</td>\n",
+       "      <td>≥ 8</td>\n",
+       "      <td>4</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5</th>\n",
+       "      <td>Meropenem</td>\n",
+       "      <td>≤ 2</td>\n",
+       "      <td>≥ 8</td>\n",
+       "      <td>4</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>6</th>\n",
+       "      <td>Doripenem</td>\n",
+       "      <td>≤ 2</td>\n",
+       "      <td>≥ 8</td>\n",
+       "      <td>4</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7</th>\n",
+       "      <td>Ciprofloxacin</td>\n",
+       "      <td>≤ 1</td>\n",
+       "      <td>≥ 4</td>\n",
+       "      <td>2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>8</th>\n",
+       "      <td>Levofloxacin</td>\n",
+       "      <td>≤ 2</td>\n",
+       "      <td>≥ 8</td>\n",
+       "      <td>4</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>9</th>\n",
+       "      <td>Piperacillin/ tazobactam</td>\n",
+       "      <td>≤ 16/4</td>\n",
+       "      <td>≥ 128/4</td>\n",
+       "      <td>32/4-64/4</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>10</th>\n",
+       "      <td>Ticarcillin/ clavulanic acid</td>\n",
+       "      <td>≤ 16/2</td>\n",
+       "      <td>≥ 128/2</td>\n",
+       "      <td>32/2-64/2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>11</th>\n",
+       "      <td>Cefotaxime</td>\n",
+       "      <td>≤ 8</td>\n",
+       "      <td>≥ 64</td>\n",
+       "      <td>16-32</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>12</th>\n",
+       "      <td>Ceftriaxone</td>\n",
+       "      <td>≤ 8</td>\n",
+       "      <td>≥ 64</td>\n",
+       "      <td>16-32</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>13</th>\n",
+       "      <td>Ceftazidime</td>\n",
+       "      <td>≤ 8</td>\n",
+       "      <td>≥ 32</td>\n",
+       "      <td>16</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>14</th>\n",
+       "      <td>Cefepime</td>\n",
+       "      <td>≤ 8</td>\n",
+       "      <td>≥ 32</td>\n",
+       "      <td>16</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>15</th>\n",
+       "      <td>Trimethoprim/ sulfamethoxazole</td>\n",
+       "      <td>≤ 2/38</td>\n",
+       "      <td>≥ 4/76</td>\n",
+       "      <td>-</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>16</th>\n",
+       "      <td>Ampicillin/ sulbactam</td>\n",
+       "      <td>≤ 8/4</td>\n",
+       "      <td>≥ 32/16</td>\n",
+       "      <td>16/8</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>17</th>\n",
+       "      <td>Colistin</td>\n",
+       "      <td>-</td>\n",
+       "      <td>≥ 4</td>\n",
+       "      <td>≤ 2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>18</th>\n",
+       "      <td>Polymyxin B</td>\n",
+       "      <td>-</td>\n",
+       "      <td>≥ 4</td>\n",
+       "      <td>≤ 2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>19</th>\n",
+       "      <td>Tetracycline</td>\n",
+       "      <td>≤ 4</td>\n",
+       "      <td>≥ 16</td>\n",
+       "      <td>8</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>20</th>\n",
+       "      <td>Doxycycline</td>\n",
+       "      <td>≤ 4</td>\n",
+       "      <td>≥ 16</td>\n",
+       "      <td>8</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>21</th>\n",
+       "      <td>Minocycline</td>\n",
+       "      <td>≤ 4</td>\n",
+       "      <td>≥ 16</td>\n",
+       "      <td>8</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                       Antibiotics Susceptible Resistant Intermediate\n",
+       "0                         Amikacin        ≤ 16      ≥ 64           32\n",
+       "1                       Tobramycin         ≤ 4      ≥ 16            8\n",
+       "2                       Gentamicin         ≤ 4      ≥ 16            8\n",
+       "3                       Netilmicin         ≤ 8      ≥ 32           16\n",
+       "4                         Imipenem         ≤ 2       ≥ 8            4\n",
+       "5                        Meropenem         ≤ 2       ≥ 8            4\n",
+       "6                        Doripenem         ≤ 2       ≥ 8            4\n",
+       "7                    Ciprofloxacin         ≤ 1       ≥ 4            2\n",
+       "8                     Levofloxacin         ≤ 2       ≥ 8            4\n",
+       "9         Piperacillin/ tazobactam      ≤ 16/4   ≥ 128/4    32/4-64/4\n",
+       "10    Ticarcillin/ clavulanic acid      ≤ 16/2   ≥ 128/2    32/2-64/2\n",
+       "11                      Cefotaxime         ≤ 8      ≥ 64        16-32\n",
+       "12                     Ceftriaxone         ≤ 8      ≥ 64        16-32\n",
+       "13                     Ceftazidime         ≤ 8      ≥ 32           16\n",
+       "14                        Cefepime         ≤ 8      ≥ 32           16\n",
+       "15  Trimethoprim/ sulfamethoxazole      ≤ 2/38    ≥ 4/76            -\n",
+       "16           Ampicillin/ sulbactam       ≤ 8/4   ≥ 32/16         16/8\n",
+       "17                        Colistin           -       ≥ 4          ≤ 2\n",
+       "18                     Polymyxin B           -       ≥ 4          ≤ 2\n",
+       "19                    Tetracycline         ≤ 4      ≥ 16            8\n",
+       "20                     Doxycycline         ≤ 4      ≥ 16            8\n",
+       "21                     Minocycline         ≤ 4      ≥ 16            8"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "clsi_bp\n",
+    "#strain_mic"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "860505f7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# convert MIC to numbers sMIC, rMIC\n",
+    "clsi_bp['s_mic'] =clsi_bp[['Susceptible']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n",
+    "clsi_bp['r_mic'] =clsi_bp[['Resistant']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n",
+    "clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "id": "cad964a6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "id": "2b6c02f5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Read only numbers in MIC values\n",
+    "#try:\n",
+    "strain_mic['o_mic']=strain_mic[['MIC']].applymap(lambda x: (re.sub(r'[^0-9.\\/]','', x)))\n",
+    "#except TypeError:\n",
+    "#    print('Waring: Error in MIC value')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "id": "942fefb2",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Strain name</th>\n",
+       "      <th>Antibiotics</th>\n",
+       "      <th>MIC</th>\n",
+       "      <th>o_mic</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>Acinetobacter baumannii A85</td>\n",
+       "      <td>Colistin</td>\n",
+       "      <td>0.1</td>\n",
+       "      <td>0.1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>Acinetobacter baumannii A85</td>\n",
+       "      <td>Colistin</td>\n",
+       "      <td>1</td>\n",
+       "      <td>1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>Acinetobacter baumannii A85</td>\n",
+       "      <td>Colistin</td>\n",
+       "      <td>2</td>\n",
+       "      <td>2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Ampicillin</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Ampicillin/sulbactam</td>\n",
+       "      <td>mg/L</td>\n",
+       "      <td>/</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Piperacillin/tazobactam</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>6</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Cefazolin</td>\n",
+       "      <td>64</td>\n",
+       "      <td>64</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Ceftriaxone</td>\n",
+       "      <td>16</td>\n",
+       "      <td>16</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>8</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Cefepime</td>\n",
+       "      <td>8</td>\n",
+       "      <td>8</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>9</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Meropenem</td>\n",
+       "      <td>0.25</td>\n",
+       "      <td>0.25</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>10</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Imipenem</td>\n",
+       "      <td>1</td>\n",
+       "      <td>1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>11</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Tigecycline</td>\n",
+       "      <td>0.5</td>\n",
+       "      <td>0.5</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>12</th>\n",
+       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
+       "      <td>Ceftazidime</td>\n",
+       "      <td>&gt;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>&gt;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>&gt;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>&gt;=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>&gt;=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>&gt;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>&gt;=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>&gt;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>&gt;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>&gt;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>&gt;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>&gt;=128/2</td>\n",
+       "      <td>128/2</td>\n",
+       "      <td>16/2</td>\n",
+       "      <td>128/2</td>\n",
+       "      <td>32/2-64/2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>19</th>\n",
+       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0305</td>\n",
+       "      <td>Polymyxinb</td>\n",
+       "      <td>1</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-</td>\n",
+       "      <td>4</td>\n",
+       "      <td>2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>20</th>\n",
+       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0306</td>\n",
+       "      <td>Polymyxinb</td>\n",
+       "      <td>1</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-</td>\n",
+       "      <td>4</td>\n",
+       "      <td>2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>21</th>\n",
+       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0307</td>\n",
+       "      <td>Polymyxinb</td>\n",
+       "      <td>8</td>\n",
+       "      <td>8</td>\n",
+       "      <td>-</td>\n",
+       "      <td>4</td>\n",
+       "      <td>2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>22</th>\n",
+       "      <td>Acinetobacter baumannii strain FDA-CDC-AR_0308</td>\n",
+       "      <td>Polymyxinb</td>\n",
+       "      <td>4</td>\n",
+       "      <td>4</td>\n",
+       "      <td>-</td>\n",
+       "      <td>4</td>\n",
+       "      <td>2</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                                       Strain name  \\\n",
+       "0                      Acinetobacter baumannii A85   \n",
+       "1                      Acinetobacter baumannii A85   \n",
+       "2                      Acinetobacter baumannii A85   \n",
+       "3                    Acinetobacter baumannii DU202   \n",
+       "4               Acinetobacter baumannii AB307-0294   \n",
+       "5                    Acinetobacter baumannii DU202   \n",
+       "6               Acinetobacter baumannii AB307-0294   \n",
+       "7                    Acinetobacter baumannii DU202   \n",
+       "8                   Acinetobacter baumannii ORAB01   \n",
+       "9               Acinetobacter baumannii AB307-0294   \n",
+       "10              Acinetobacter baumannii AB307-0294   \n",
+       "11               Acinetobacter baumannii AB5075-UW   \n",
+       "12              Acinetobacter baumannii AB307-0294   \n",
+       "13              Acinetobacter baumannii AB307-0294   \n",
+       "14               Acinetobacter baumannii AB5075-UW   \n",
+       "15               Acinetobacter baumannii AB5075-UW   \n",
+       "16                   Acinetobacter baumannii DU202   \n",
+       "17                   Acinetobacter baumannii DU202   \n",
+       "18                   Acinetobacter baumannii DU202   \n",
+       "19  Acinetobacter baumannii strain FDA-CDC-AR_0305   \n",
+       "20  Acinetobacter baumannii strain FDA-CDC-AR_0306   \n",
+       "21  Acinetobacter baumannii strain FDA-CDC-AR_0307   \n",
+       "22  Acinetobacter baumannii strain FDA-CDC-AR_0308   \n",
+       "\n",
+       "                      Antibiotics         MIC  o_mic s_mic  r_mic      i_mic  \n",
+       "0                        Colistin         0.1    0.1     -      4          2  \n",
+       "1                        Colistin           1      1     -      4          2  \n",
+       "2                        Colistin           2      2     -      4          2  \n",
+       "3                        Colistin                        -      4          2  \n",
+       "4            Ampicillin/sulbactam        mg/L      /   8/4  32/16       16/8  \n",
+       "5            Ampicillin/sulbactam  >=0.3 mg/L   0.3/   8/4  32/16       16/8  \n",
+       "6         Piperacillin/tazobactam           0      0  16/4  128/4  32/4-64/4  \n",
+       "7         Piperacillin/tazobactam          NA         16/4  128/4  32/4-64/4  \n",
+       "8         Piperacillin/tazobactam       >64/4   64/4  16/4  128/4  32/4-64/4  \n",
+       "9                     Ceftriaxone          16     16     8     64      16-32  \n",
+       "10                       Cefepime           8      8     8     32         16  \n",
+       "11                       Cefepime        >256    256     8     32         16  \n",
+       "12                      Meropenem        0.25   0.25     2      8          4  \n",
+       "13                       Imipenem           1      1     2      8          4  \n",
+       "14                    Ceftazidime        >128    128     8     32         16  \n",
+       "15                  Ciprofloxacin         >32     32     1      4          2  \n",
+       "16  Trimethoprim/sulfamethoxazole       8/152  8/152  2/38   4/76          -  \n",
+       "17  Trimethoprim/sulfamethoxazole       8/152  8/152  2/38   4/76          -  \n",
+       "18     Ticarcillin/clavulanicacid     >=128/2  128/2  16/2  128/2  32/2-64/2  \n",
+       "19                     Polymyxinb           1      1     -      4          2  \n",
+       "20                     Polymyxinb           1      1     -      4          2  \n",
+       "21                     Polymyxinb           8      8     -      4          2  \n",
+       "22                     Polymyxinb           4      4     -      4          2  "
+      ]
+     },
+     "execution_count": 53,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "#compare CLSI Antibiotics only\n",
+    "#result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner',  indicator=True)[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','_merge']]\n",
+    "try:\n",
+    "    result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner')[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','i_mic']]\n",
+    "except KeyError:\n",
+    "    print('Waring: Error in input Values')\n",
+    "result"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 44,
+   "id": "44f7e35d",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "ValueError",
+     "evalue": "could not broadcast input array from shape (23,) into shape (23,1)",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-44-76a7d8475ba3>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m#compare MIC values and assign Susceptible and Resistant to Strain\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0;31m#try:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mresult\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'CLSI_profile'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'o_mic'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m's_mic'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m'r_mic'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m'i_mic'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msus_res\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0maxis\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      4\u001b[0m \u001b[0;31m#except ValueError:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;31m#    print('Waring: Error in input MIC value')\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36m__setitem__\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m   3158\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_frame\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3159\u001b[0m         \u001b[0;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mSeries\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndarray\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mIndex\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3160\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_array\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   3161\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3162\u001b[0m             \u001b[0;31m# set column\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36m_setitem_array\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m   3196\u001b[0m                 )[1]\n\u001b[1;32m   3197\u001b[0m                 \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_check_setitem_copy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3198\u001b[0;31m                 \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0miloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   3199\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3200\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_setitem_frame\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m__setitem__\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m    690\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    691\u001b[0m         \u001b[0miloc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"iloc\"\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0miloc\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 692\u001b[0;31m         \u001b[0miloc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_with_indexer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    693\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    694\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_validate_key\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m_setitem_with_indexer\u001b[0;34m(self, indexer, value, name)\u001b[0m\n\u001b[1;32m   1635\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_with_indexer_split_path\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1636\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-> 1637\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setitem_single_block\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1638\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1639\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_setitem_with_indexer_split_path\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/indexing.py\u001b[0m in \u001b[0;36m_setitem_single_block\u001b[0;34m(self, indexer, value, name)\u001b[0m\n\u001b[1;32m   1859\u001b[0m         \u001b[0;31m# actually do the set\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1860\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_consolidate_inplace\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-> 1861\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_mgr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_mgr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetitem\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m=\u001b[0m\u001b[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   1862\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_maybe_update_cacher\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mclear\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1863\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/internals/managers.py\u001b[0m in \u001b[0;36msetitem\u001b[0;34m(self, indexer, value)\u001b[0m\n\u001b[1;32m    566\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    567\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0msetitem\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;34m\"BlockManager\"\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 568\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"setitem\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindexer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m=\u001b[0m\u001b[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    569\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    570\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mputmask\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmask\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnew\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0malign\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mbool\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/internals/managers.py\u001b[0m in \u001b[0;36mapply\u001b[0;34m(self, f, align_keys, ignore_failures, **kwargs)\u001b[0m\n\u001b[1;32m    425\u001b[0m                     \u001b[0mapplied\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    426\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--> 427\u001b[0;31m                     \u001b[0mapplied\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mb\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\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    428\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mTypeError\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mNotImplementedError\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[1;32m    429\u001b[0m                 \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mignore_failures\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pandas/core/internals/blocks.py\u001b[0m in \u001b[0;36msetitem\u001b[0;34m(self, indexer, value)\u001b[0m\n\u001b[1;32m   1033\u001b[0m         \u001b[0;31m# set\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1034\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1035\u001b[0;31m             \u001b[0mvalues\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1036\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1037\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mtranspose\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mValueError\u001b[0m: could not broadcast input array from shape (23,) into shape (23,1)"
+     ]
+    }
+   ],
+   "source": [
+    "#compare MIC values and assign Susceptible and Resistant to Strain\n",
+    "#try:\n",
+    "result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res,axis = 1)\n",
+    "#except ValueError:\n",
+    "#    print('Waring: Error in input MIC value')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 61,
+   "id": "30c2a7a3",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Strain name</th>\n",
+       "      <th>Antibiotics</th>\n",
+       "      <th>MIC</th>\n",
+       "      <th>o_mic</th>\n",
+       "      <th>s_mic</th>\n",
+       "      <th>r_mic</th>\n",
+       "      <th>i_mic</th>\n",
+       "      <th>CLSI_profile</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>Acinetobacter baumannii A85</td>\n",
+       "      <td>Colistin</td>\n",
+       "      <td>0.1</td>\n",
+       "      <td>0.1</td>\n",
+       "      <td>-</td>\n",
+       "      <td>4</td>\n",
+       "      <td>2</td>\n",
+       "      <td>Intermediate</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>Acinetobacter baumannii A85</td>\n",
+       "      <td>Colistin</td>\n",
+       "      <td>1</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-</td>\n",
+       "      <td>4</td>\n",
+       "      <td>2</td>\n",
+       "      <td>Intermediate</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>Acinetobacter baumannii A85</td>\n",
+       "      <td>Colistin</td>\n",
+       "      <td>2</td>\n",
+       "      <td>2</td>\n",
+       "      <td>-</td>\n",
+       "      <td>4</td>\n",
+       "      <td>2</td>\n",
+       "      <td>IntermediatE</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>Acinetobacter baumannii DU202</td>\n",
+       "      <td>Colistin</td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "      <td>-</td>\n",
+       "      <td>4</td>\n",
+       "      <td>2</td>\n",
+       "      <td>Strain could not classified</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Ampicillin/sulbactam</td>\n",
+       "      <td>mg/L</td>\n",
+       "      <td>/</td>\n",
+       "      <td>8/4</td>\n",
+       "      <td>32/16</td>\n",
+       "      <td>16/8</td>\n",
+       "      <td>Strain could not classified</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5</th>\n",
+       "      <td>Acinetobacter baumannii DU202</td>\n",
+       "      <td>Ampicillin/sulbactam</td>\n",
+       "      <td>&gt;=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>&gt;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>&gt;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>&gt;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>&gt;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>&gt;=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
+}
diff -r 000000000000 -r c1a77856070c clsi_profile_type2_linux.ipynb
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clsi_profile_type2_linux.ipynb	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,1040 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 37,
+   "id": "9aa0a6f7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics\n",
+    "# By rakesh4osdd@gmail.com, 06-Jun-2021\n",
+    "import pandas as pd\n",
+    "import re\n",
+    "import sys"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 38,
+   "id": "9af8387e",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "1.2.4 2.2.1\n"
+     ]
+    }
+   ],
+   "source": [
+    "#print(pd.__version__, re.__version__)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 39,
+   "id": "73d0783c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# compare two MIC value strings\n",
+    "def check_mic(mic1,mic2,mic_type):\n",
+    "    #print(mic1,mic2,mic_type)\n",
+    "    try:\n",
+    "        if '/' in mic1:\n",
+    "            m1a = mic1.split('/')[0]\n",
+    "            m1b = mic1.split('/')[1]\n",
+    "            if float(m1a)==0 or float(m1b)==0:\n",
+    "                strain_type='Strain could not be classified'\n",
+    "                return(strain_type)          \n",
+    "        elif '/' in mic2:\n",
+    "            m1a = mic1\n",
+    "            if float(m1a)==0:\n",
+    "                strain_type='Strain could not be classified'\n",
+    "                return(strain_type)            \n",
+    "            m1b = '1'\n",
+    "        elif float(mic1)==0:\n",
+    "            strain_type='Strain could not be classified'\n",
+    "            return(strain_type)\n",
+    "        else:\n",
+    "            m1a = mic1\n",
+    "            \n",
+    "        if '-' in mic2:\n",
+    "            m2a = mic2.split('-')[0]\n",
+    "            m2b = mic2.split('-')[1]           \n",
+    "         \n",
+    "    except ValueError:\n",
+    "        strain_type='Strain could not be classified' \n",
+    "        return(strain_type)\n",
+    "    try:\n",
+    "        if '-' in mic2 and mic_type == 'i':   # for intermediate only\n",
+    "            if '/' in mic2:\n",
+    "                m2a = mic2.split('-')[0].split('/')[0]\n",
+    "                m2b = mic2.split('-')[0].split('/')[1]\n",
+    "                m2aa = mic2.split('-')[1].split('/')[0]\n",
+    "                m2bb = mic2.split('-')[1].split('/')[1]\n",
+    "                if (float(m2aa)>=float(m1a)>=float(m2a) and float(m2bb)>=float(m1b)>=float(m2b)):\n",
+    "                    #print('intermediate')\n",
+    "                    m_type='Intermediate'\n",
+    "                else:\n",
+    "                    #print('not define')\n",
+    "                    m_type='Strain could not be classified'\n",
+    "            else:\n",
+    "                m2a = mic2.split('-')[0]\n",
+    "                m2b = mic2.split('-')[1] \n",
+    "                if (float(m2b)>=float(m1a)>=float(m2a)):\n",
+    "                    #print('intermediate')\n",
+    "                    m_type='Intermediate'\n",
+    "                else:\n",
+    "                    #print('not define')\n",
+    "                    m_type='Strain could not be classified'                \n",
+    "            #print (m1a,m1b,m2a,m2b,m2aa,m2bb)\n",
+    "        elif '/' in mic2:\n",
+    "            m2a = mic2.split('/')[0]\n",
+    "            m2b = mic2.split('/')[1]\n",
+    "            #print(m1a,m1b,m2a,m2b,mic_type)\n",
+    "            if (mic_type=='s' and (float(m1a)<=float(m2a) and float(m1b)<=float(m2b))):\n",
+    "                m_type='Susceptible'\n",
+    "            elif (mic_type=='r' and (float(m1a)>=float(m2a) and float(m1b)>=float(m2b))):\n",
+    "                m_type='Resistant'\n",
+    "            elif (mic_type=='i' and (float(m1a)==float(m2a) and float(m1b)==float(m2b))):\n",
+    "                m_type='Intermediate'\n",
+    "            else:\n",
+    "                m_type='Strain could not be classified'\n",
+    "        elif '-' in mic2:\n",
+    "                m_type='Strain could not be classified'\n",
+    "        else:\n",
+    "            m2a=mic2\n",
+    "            if (mic_type=='s' and (float(m1a)<=float(m2a))):\n",
+    "                m_type='Susceptible'\n",
+    "            elif (mic_type=='r' and (float(m1a)>=float(m2a))):\n",
+    "                m_type='Resistant'\n",
+    "            elif (mic_type=='i' and (float(m1a)==float(m2a))):\n",
+    "                m_type='Intermediate'\n",
+    "            else:\n",
+    "                m_type='Strain could not be classified-1'        \n",
+    "    except IndexError:\n",
+    "        strain_type='Strain could not be classified-2' \n",
+    "        return(strain_type)\n",
+    "    \n",
+    "    return(m_type)\n",
+    "\n",
+    "#check_mic('65','32-64','i')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 40,
+   "id": "4d2ab1b1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# compare MIC value in pandas list\n",
+    "def sus_res_int(mic):\n",
+    "    #print(mic)\n",
+    "    o_mic = mic[0].replace(' ', '')\n",
+    "    s_mic = mic[1].replace(' ', '')\n",
+    "    r_mic = mic[2].replace(' ', '')\n",
+    "    i_mic = mic[3].replace(' ', '')\n",
+    "    try:\n",
+    "        if check_mic(o_mic,s_mic,'s')=='Susceptible':\n",
+    "            strain_type='Susceptible'\n",
+    "        elif check_mic(o_mic,r_mic,'r')=='Resistant':\n",
+    "            strain_type='Resistant'\n",
+    "        elif check_mic(o_mic,i_mic,'i')=='Intermediate':\n",
+    "            strain_type='Intermediate'                    \n",
+    "        else:\n",
+    "            strain_type='Strain could not be classified'\n",
+    "    except ValueError:\n",
+    "        strain_type='Strain could not be classified'            \n",
+    "    return(strain_type)\n",
+    "\n",
+    "#mic=['128','16/4','128/4','32/4-64/4']\n",
+    "#sus_res_int(mic)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 41,
+   "id": "0e22ef0d",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'# for input argument\\ninput_user = sys.argv[1]\\ninput_clsi = sys.argv[2]\\noutput_table = sys.argv[3]'"
+      ]
+     },
+     "execution_count": 41,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# for input argument\n",
+    "input_user = sys.argv[1]\n",
+    "input_clsi = sys.argv[2]\n",
+    "output_table = sys.argv[3]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 42,
+   "id": "21d5fe63",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "'''input_user='input2.csv'\n",
+    "input_clsi='clsi.csv'\n",
+    "output_profile=input_user+'_profile.csv'\n",
+    "output_table=input_user+'_table.csv''''"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 43,
+   "id": "1e64b025",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Strain name</th>\n",
+       "      <th>Antibiotics</th>\n",
+       "      <th>MIC</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>Acinetobacter baumannii A85</td>\n",
+       "      <td>Colistin</td>\n",
+       "      <td>0.1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>Acinetobacter baumannii A85</td>\n",
+       "      <td>Netilmicin</td>\n",
+       "      <td>1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Ampicillin</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Ampicillin/sulbactam</td>\n",
+       "      <td>mg/L</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>piperacillin/tazobactam</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Cefazolin</td>\n",
+       "      <td>64</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>6</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Ceftriaxone</td>\n",
+       "      <td>16</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Cefepime</td>\n",
+       "      <td>8</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>8</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Meropenem</td>\n",
+       "      <td>0.25</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>9</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Imipenem</td>\n",
+       "      <td>1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>10</th>\n",
+       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
+       "      <td>Tigecycline</td>\n",
+       "      <td>0.5</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>11</th>\n",
+       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
+       "      <td>Ceftazidime</td>\n",
+       "      <td>&gt;128</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>12</th>\n",
+       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
+       "      <td>Cefepime</td>\n",
+       "      <td>&gt;256</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>13</th>\n",
+       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
+       "      <td>Ciprofloxacin</td>\n",
+       "      <td>&gt;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>&gt;=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>&gt;=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>&gt;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>&gt;=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>&gt;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>&gt;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>&gt;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>&gt;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>&gt;=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
+}
diff -r 000000000000 -r c1a77856070c input.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/input.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,31 @@
+id,genome Ids,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit
+470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L
+470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,1,mg/L
+470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,2,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L
+470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L
+470,CP008706.1,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L
+470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
+470,CP015483.1,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L
+470,470.7601,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,470.7651,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,470.7764,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,470.8071,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,470.7405,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L
+470,470.7406,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L
+470,470.7407,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L
+470,470.7408,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
diff -r 000000000000 -r c1a77856070c input.csv_table.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/input.csv_table.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,10 @@
+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
diff -r 000000000000 -r c1a77856070c output.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/output.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,10 @@
+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
diff -r 000000000000 -r c1a77856070c test-data/asist_input.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/asist_input.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,5 @@
+Strain name,Resistance_phenotype,Amikacin,Tobramycin,Gentamycin,Imipenem,Meropenam,Doripenem,Ciprofloxacin,Levofloxacin,Piperacillin/tazobactam,Ticarcillin/clavulanic acid,Cefotaxime,Ceftriaxone,Ceftazidime,Cefepime,Trimethoprim/sulfamethoxazole,Ampicillin/sulbactam,Colistin,polymyxin B,Tetracycline,Doxicycline ,Minocycline
+Strain name,Resistance_phenotype,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems,Beta-lactams-Carbapenems,Carbapenem ,Fluoroquinolone,Fluoroquinolone,Beta-lactam inhibitor,Beta-lactam inhibitor,Cephalosporin,Cephalosporin,Cephalosporin,Cephalosporin,Sulfonamides,Penicillins/beta-lactamase,Polymyxins,Polymyxins,Tetracycline,Tetracycline,Tetracycline
+Acinetobacter baumannii strain FDA-CDC-AR_0288,,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant
+Acinetobacter baumannii strain FDA-CDC-AR_0303,,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,NA
+Acinetobacter baumannii strain FDA-CDC-AR_0304,,NA,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant
diff -r 000000000000 -r c1a77856070c test-data/asist_output.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/asist_output.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,5 @@
+Strain name,Strain phenotype,Resistance_phenotype,Amikacin,Tobramycin,Gentamycin,Imipenem,Meropenam,Doripenem,Ciprofloxacin,Levofloxacin,Piperacillin/ tazobactam,Ticarcillin/ clavulanic acid,Cefotaxime,Ceftriaxone,Ceftazidime,Cefepime,Trimethoprim/ sulfamethoxazole,Ampicillin/ sulbactam,Colistin,Polymyxin B,Tetracycline,Doxicycline,Minocycline
+Strain name,Strain could not be classified,Resistance_phenotype,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems,Beta-lactams-Carbapenems,Carbapenem ,Fluoroquinolone,Fluoroquinolone,Beta-lactam inhibitor,Beta-lactam inhibitor,Cephalosporin,Cephalosporin,Cephalosporin,Cephalosporin,Sulfonamides,Penicillins/beta-lactamase,Polymyxins,Polymyxins,Tetracycline,Tetracycline,Tetracycline
+Acinetobacter baumannii strain FDA-CDC-AR_0288,Possible TDR,,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant
+Acinetobacter baumannii strain FDA-CDC-AR_0303,Possible TDR,,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,NA
+Acinetobacter baumannii strain FDA-CDC-AR_0304,Possible TDR,,NA,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,Resistant,NA,Resistant
diff -r 000000000000 -r c1a77856070c test-data/clsi.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clsi.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,23 @@
+Antibiotics,Susceptible,Resistant,Intermediate
+Amikacin,≤ 16,≥ 64,32
+Tobramycin,≤ 4,≥ 16,8
+Gentamicin,≤ 4,≥ 16,8
+Netilmicin,≤ 8,≥ 32,16
+Imipenem,≤ 2,≥ 8,4
+Meropenem,≤ 2,≥ 8,4
+Doripenem,≤ 2,≥ 8,4
+Ciprofloxacin,≤ 1,≥ 4,2
+Levofloxacin,≤ 2,≥ 8,4
+Piperacillin/ tazobactam,≤ 16/4,≥ 128/4,32/4-64/4
+Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2,32/2-64/2
+Cefotaxime,≤ 8,≥ 64,16-32
+Ceftriaxone,≤ 8,≥ 64,16-32
+Ceftazidime,≤ 8,≥ 32,16
+Cefepime,≤ 8,≥ 32,16
+Trimethoprim/ sulfamethoxazole,≤ 2/38,≥ 4/76,-
+Ampicillin/ sulbactam,≤ 8/4,≥ 32/16,16/8
+Colistin,-,≥ 4,≤ 2
+Polymyxin B,-,≥ 4,≤ 2
+Tetracycline,≤ 4,≥ 16,8
+Doxycycline,≤ 4,≥ 16,8
+Minocycline,≤ 4,≥ 16,8
\ No newline at end of file
diff -r 000000000000 -r c1a77856070c test-data/input.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,31 @@
+id,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit
+470,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L
+470,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,1,mg/L
+470,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,2,mg/L
+470,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L
+470,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L
+470,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L
+470,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L
+470,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L
+470,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L
+470,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L
+470,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L
+470,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L
+470,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L
+470,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L
+470,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L
+470,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L
+470,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
+470,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L
+470,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L
+470,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L
+470,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
+470,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L
+470,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L
+470,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L
+470,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L
+470,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
diff -r 000000000000 -r c1a77856070c test-data/input2.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input2.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,29 @@
+id,genome Ids,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit
+470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L
+470,CP021782.1,Acinetobacter baumannii A85,Netilmicin,Susceptible ,NA,1,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L
+470,CP001172.2,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L
+470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L
+470,CP008706.1,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L
+470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L
+470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
+470,CP015483.1,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L
+470,470.7601,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,470.7651,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,470.7764,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,470.8071,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
+470,470.7405,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L
+470,470.7406,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L
+470,470.7407,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L
+470,470.7408,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
diff -r 000000000000 -r c1a77856070c test-data/output.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.csv	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,10 @@
+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
diff -r 000000000000 -r c1a77856070c tool.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool.sh	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,15 @@
+#!/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
diff -r 000000000000 -r c1a77856070c tool_asist.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_asist.sh	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+planemo tool_init --id 'asist' --name 'ASIST' --version 1.0.1 \
+          --description 'Antimicrobial Susceptibility standards based phenotypes' \
+          --requirement 'pandas' \
+          --example_command "\"${__tool_directory__}/asist_dynamic.py\" 'asist_input.csv'  'asist_output.csv'" \
+          --example_input test-data/asist_input.csv \
+          --example_output test-data/asist_output.csv \
+          --test_case \
+	  --version_command 'python -c "import pandas; print(pandas.__version__)"' \
+          --doi 'https://ab-openlab.csir.res.in/asist'
+
+planemo lint asist.xml
diff -r 000000000000 -r c1a77856070c tool_shed.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_shed.sh	Sat Jun 26 07:27:53 2021 +0000
@@ -0,0 +1,4 @@
+#!/bin/bash
+# After reviewing .shed.yml, this configuration file and relevant shed artifacts can be quickly linted using the following command.
+planemo shed_lint --tools
+planemo shed_create --shed_target toolshed