changeset 1:c5ffaf5288fe draft

Deleted selected files
author rakesh4osdd
date Fri, 11 Jun 2021 13:19:48 +0000
parents 62226cd1acb5
children 306236ec0511
files clsi_profile_type2.py clsi_profile_type2_linux-Copy1.ipynb clsi_profile_type2_linux.ipynb dump/clsi.csv dump/clsi_profile.xml dump/clsi_profile_comb.csv dump/input.csv dump/input_ast_comb2.csv dump/input_ast_comb2.csv_table.csv dump/output.csv
diffstat 10 files changed, 0 insertions(+), 3316 deletions(-) [+]
line wrap: on
line diff
--- a/clsi_profile_type2.py	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,244 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-# In[1245]:
-
-
-# ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics
-# By rakesh4osdd@gmail.com, 06-Jun-2021
-import pandas as pd
-import re
-import sys
-
-
-# In[1246]:
-
-
-# cross check MIC values
-def sus_res(mic):
-    #print(mic)
-    #print ((mic,pd.isna(mic[1]),pd.isna(mic[0]),'\n')
-    if not (pd.isna(mic[0]) or pd.isna(mic[1]) or pd.isna(mic[2])):#check for NaN value
-        #remove unwanted whitespace
-        o_mic = mic[0].replace(' ', '')
-        s_mic = mic[1].replace(' ', '')
-        r_mic = mic[2].replace(' ', '')
-        #print (o_mic,s_mic,r_mic)
-        #print (type(o_mic),type(s_mic),type(r_mic))
-        if '/' in s_mic: #check for combination antibiotics
-            #print ('combination antibiotics')
-            try:
-                if '/' in o_mic:
-                    #print ('input combination')
-                    if (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(o_mic.split('/')[1]) <= float(s_mic.split('/')[1])):
-                        strain_type='Susceptible'
-                    elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(o_mic.split('/')[1]) >= float(r_mic.split('/')[1])):
-                        strain_type='Resistant'
-                    else:
-                        strain_type='Intermediate'
-                else: 
-                    #print ('single')
-                    if float(o_mic)==0:
-                        strain_type='Strain could not classified'
-                    elif (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(1) <= float(s_mic.split('/')[1])):
-                        strain_type='Susceptible'
-                    elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(1) >= float(r_mic.split('/')[1])):
-                        strain_type='Resistant'
-                    else:
-                        strain_type='Intermediate'
-            except ValueError:
-                strain_type='Strain could not classified'
-        else: #single antibiotics
-            #print('single antibiotics')
-            if o_mic:
-                if float(o_mic)==0:
-                    strain_type='Strain could not classified'
-                elif (float(o_mic) <= float(s_mic)):
-                    strain_type='Susceptible'
-                elif (float(o_mic) >= float(r_mic)):
-                    strain_type='Resistant'
-                else:
-                    strain_type='Intermediate'
-            else:
-                strain_type='Strain could not classified'
-    else:
-        strain_type='Strain could not classified'
-    return(strain_type)
-
-
-# In[ ]:
-
-# for input argument
-input_user = sys.argv[1]
-input_clsi = sys.argv[2]
-output_table = sys.argv[3]
-
-# In[1247]:
-
-
-"""
-input_user='input_ast_comb2.csv'
-input_clsi='clsi_profile_comb.csv'
-output_profile=input_user+'_profile.csv'
-output_table=input_user+'_table.csv'
-
-"""
-
-# In[1248]:
-
-
-# read user AST data with selected 3 columns
-strain_mic=pd.read_csv(input_user, sep=',', usecols =['Strain name', 'Antibiotics', 'MIC'],na_filter=False)
-
-
-# In[1249]:
-
-
-clsi_bp=pd.read_csv(input_clsi,sep=',')
-
-
-# In[1290]:
-
-
-#clsi_bp.head(2)
-#strain_mic
-
-
-# In[1251]:
-
-
-# convert MIC to numbers sMIC, rMIC
-clsi_bp['s_mic'] =clsi_bp[['Susceptible']].applymap(lambda x: (re.sub(r'[^0-9.\/]', '', x)))
-clsi_bp['r_mic'] =clsi_bp[['Resistant']].applymap(lambda x: (re.sub(r'[^0-9.\/]', '', x)))
-
-
-# In[1252]:
-
-
-# Read only numbers in MIC values
-#try:
-strain_mic['o_mic']=strain_mic[['MIC']].applymap(lambda x: (re.sub(r'[^0-9.\/]','', x)))
-#except TypeError:
-#    print('Waring: Error in MIC value')
-
-
-# In[1289]:
-
-
-#strain_mic.head()
-
-
-# In[1254]:
-
-
-# capitalize each Antibiotic Name for comparision with removing whitespace
-strain_mic['Antibiotics']=strain_mic['Antibiotics'].str.capitalize().str.replace(" ","")
-clsi_bp['Antibiotics']=clsi_bp['Antibiotics'].str.capitalize().str.replace(" ","")
-
-
-# In[1255]:
-
-
-#compare CLSI Antibiotics only
-#result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner',  indicator=True)[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','_merge']]
-try:
-    result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner')[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic']]
-except KeyError:
-    print('Waring: Error in input Values')
-
-
-# In[1256]:
-
-
-#compare MIC values and assign Susceptible and Resistant to Strain
-#try:
-result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic']].apply(sus_res,axis = 1)
-#except ValueError:
-#    print('Waring: Error in input MIC value')
-
-
-# In[1288]:
-
-
-#result
-
-
-# In[1258]:
-
-
-#result[['Strain name', 'Antibiotics', 'MIC','s_mic','r_mic','CLSI_profile']].to_csv(output_profile,sep=',', index=False, encoding='utf-8-sig')
-
-
-# In[1259]:
-
-
-#create a pivot table for ASIST
-table=result[['Strain name', 'Antibiotics','CLSI_profile']].drop_duplicates()
-result_table=pd.pivot_table(table, values ='CLSI_profile', index =['Strain name'],columns =['Antibiotics'], aggfunc = lambda x: ' '.join(x))
-
-
-# In[1261]:
-
-
-result_table
-
-
-# In[1264]:
-
-
-#result_table.to_csv(output_table,na_rep='NA')
-
-
-# In[1282]:
-
-
-# reorder the Antibiotics for ASIST
-clsi_ab=['Amikacin','Tobramycin','Gentamycin','Imipenem','Meropenem','Doripenem','Ciprofloxacin','Levofloxacin',
-         'Piperacillin/tazobactam','Ticarcillin/clavulanicacid','Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime',
-         'Trimethoprim/sulfamethoxazole','Ampicillin/sulbactam','Colistin','Polymyxinb','Tetracycline','Doxicycline ',
-         'Minocycline']
-result_selected=result_table.filter(clsi_ab)
-
-
-# In[1283]:
-
-
-result_selected.shape
-
-
-# In[1284]:
-
-
-result_table.shape
-
-
-# In[1285]:
-
-
-result_selected.insert(0,'Resistance_phenotype','')
-
-
-# In[1286]:
-
-
-result_selected.to_csv(output_table,na_rep='NA')
-
-
-# In[1287]:
-
-
-#rename headers
-result_selected.rename(columns = {'Ticarcillin/clavulanicacid':'Ticarcillin/clavulanic acid','Piperacillin/tazobactam':'Piperacillin/ tazobactam','Trimethoprim/sulfamethoxazole': 'Trimethoprim/ sulfamethoxazole','Ampicillin/sulbactam':'Ampicillin/ sulbactam', 'Polymyxinb': 'Polymyxin B'} )
-
-
-# In[ ]:
-
-
-
-
-
-# In[ ]:
-
-
-
-
--- a/clsi_profile_type2_linux-Copy1.ipynb	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2461 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "967b1345",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics\n",
-    "# By rakesh4osdd@gmail.com, 06-Jun-2021\n",
-    "import pandas as pd\n",
-    "import re\n",
-    "import sys"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "id": "39e25c15",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "1.2.4 2.2.1\n"
-     ]
-    }
-   ],
-   "source": [
-    "print(pd.__version__, re.__version__)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 175,
-   "id": "c96d7c62",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# cross check MIC values\n",
-    "def sus_res(mic):\n",
-    "    print(mic)\n",
-    "    #print ((mic,pd.isna(mic[1]),pd.isna(mic[0]),'\\n')\n",
-    "    if not (pd.isna(mic[0]) or pd.isna(mic[1]) or pd.isna(mic[2])):#check for NaN value\n",
-    "        #remove unwanted whitespace\n",
-    "        o_mic = mic[0].replace(' ', '')\n",
-    "        s_mic = mic[1].replace(' ', '')\n",
-    "        r_mic = mic[2].replace(' ', '')\n",
-    "        i_mic = mic[3].replace(' ', '')\n",
-    "        print(imic(o_mic,i_mic))\n",
-    "        #print (o_mic,s_mic,r_mic)\n",
-    "        #print (type(o_mic),type(s_mic),type(r_mic))\n",
-    "        if '/' in s_mic: #check for combination antibiotics\n",
-    "            #print ('combination antibiotics')\n",
-    "            try:\n",
-    "                if '/' in o_mic:\n",
-    "                    #print ('input combination')\n",
-    "                    if (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(o_mic.split('/')[1]) <= float(s_mic.split('/')[1])):\n",
-    "                        strain_type='Susceptible'\n",
-    "                    elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(o_mic.split('/')[1]) >= float(r_mic.split('/')[1])):\n",
-    "                        strain_type='Resistant'\n",
-    "                    elif (imic(o_mic,i_mic)):\n",
-    "                        strain_type='Intermediate-1'                    \n",
-    "                    else:\n",
-    "                        strain_type='Intermediate-2'\n",
-    "                else: \n",
-    "                    #print ('single')\n",
-    "                    if float(o_mic)==0:\n",
-    "                        strain_type='Strain could not classified'\n",
-    "                    elif (float(o_mic.split('/')[0]) <= float(s_mic.split('/')[0]) and float(1) <= float(s_mic.split('/')[1])):\n",
-    "                        strain_type='Susceptible'\n",
-    "                    elif (float(o_mic.split('/')[0]) >= float(r_mic.split('/')[0]) and float(1) >= float(r_mic.split('/')[1])):\n",
-    "                        strain_type='Resistant'\n",
-    "                    else:\n",
-    "                        strain_type='Intermediate-3'\n",
-    "            except ValueError:\n",
-    "                strain_type='Strain could not classified-1'\n",
-    "        elif (s_mic == '-'):\n",
-    "            if o_mic:\n",
-    "                if float(o_mic)==0:\n",
-    "                    strain_type='Strain could not classified-2'\n",
-    "                #elif (float(o_mic) <= float(s_mic)):\n",
-    "                #    strain_type='Susceptible'\n",
-    "                elif (float(o_mic) >= float(r_mic)):\n",
-    "                    strain_type='Resistant'\n",
-    "                elif (imic(o_mic,i_mic)):\n",
-    "                    strain_type='Intermediat-4'\n",
-    "                else:\n",
-    "                    strain_type='Intermediate-5'\n",
-    "            else:\n",
-    "                strain_type='Strain could not classified-3'\n",
-    "        else: #single antibiotics\n",
-    "            #print('single antibiotics')\n",
-    "            if o_mic:\n",
-    "                if float(o_mic)==0:\n",
-    "                    strain_type='Strain could not classified-4'\n",
-    "                elif (float(o_mic) <= float(s_mic)):\n",
-    "                    strain_type='Susceptible'\n",
-    "                elif (float(o_mic) >= float(r_mic)):\n",
-    "                    strain_type='Resistant'\n",
-    "                else:\n",
-    "                    strain_type='Intermediate-6'\n",
-    "            else:\n",
-    "                strain_type='Strain could not classified-5'\n",
-    "    else:\n",
-    "        strain_type='Strain could not classified-6'\n",
-    "    return(strain_type)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 176,
-   "id": "dbc70e34",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "['32/2', '16/4', '128/4', '32/4-64/4']\n",
-      "32/2 32/4-64/4\n",
-      "False\n",
-      "32/2 32/4-64/4\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "'Intermediate-2'"
-      ]
-     },
-     "execution_count": 176,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "mic=['32/2','16/4','128/4','32/4-64/4']\n",
-    "sus_res(mic)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "653b096e",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 202,
-   "id": "626a1e3f",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "65/4 64/4 s\n",
-      "65 4 64 4 s\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "'Strain could not classified-5'"
-      ]
-     },
-     "execution_count": 202,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "def check_mic(mic1,mic2,mic_type):\n",
-    "    print(mic1,mic2,mic_type)\n",
-    "    m1a = mic1.split('/')[0]\n",
-    "    m1b = mic1.split('/')[1]\n",
-    "    if '-' in mic2:   # for intermediate only\n",
-    "        m2a = mic2.split('-')[0].split('/')[0]\n",
-    "        m2b = mic2.split('-')[0].split('/')[1]\n",
-    "        m2aa = mic2.split('-')[1].split('/')[0]\n",
-    "        m2bb = mic2.split('-')[1].split('/')[1]\n",
-    "        if (float(m2aa)>=float(m1a)>=float(m2a) and float(m2b)>=float(m1b)>=float(m2b)):\n",
-    "            #print('intermediate')\n",
-    "            mic_type='Intermediate-1'\n",
-    "        else:\n",
-    "            #print('not define')\n",
-    "            mic_type='Strain could not classified-1'\n",
-    "        #print (m1a,m1b,m2a,m2b,m2aa,m2bb)\n",
-    "    else:\n",
-    "        m2a = mic2.split('/')[0]\n",
-    "        m2b = mic2.split('/')[1]\n",
-    "        print(m1a,m1b,m2a,m2b,mic_type)\n",
-    "        if mic_type=='s':\n",
-    "            if (float(m1a)<=float(m2a) and float(m1b)<=float(m2b)):\n",
-    "                mic_type='Susceptible'\n",
-    "            else:\n",
-    "                mic_type='Strain could not classified-5'\n",
-    "        elif mic_type=='r':\n",
-    "            if (float(m1a)>=float(m2a) and float(m1b)>=float(m2b)):\n",
-    "                mic_type='Resistant'\n",
-    "            else:\n",
-    "                mic_type='Strain could not classified-4'\n",
-    "        elif mic_type=='i':\n",
-    "            if (float(m1a)==float(m2a) and float(m1b)==float(m2b)):\n",
-    "                mic_type='Intermediate-2'\n",
-    "            else:\n",
-    "                mic_type='Strain could not classified-3'\n",
-    "        else:\n",
-    "            mic_type='Strain could not classified-2'\n",
-    "    return(mic_type)\n",
-    "        \n",
-    "check_mic('65/4','64/4','s')\n",
-    "#    float(mic1.split('/')[0]) <= float(mic2.split('/')[0]) and float(mic1.split('/')[1]) <= float(mic2.split('/')[1])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 171,
-   "id": "19905924",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#compare MIC values and assign Susceptible and Resistant to Strain\n",
-    "#try:\n",
-    "#result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res,axis = 1)\n",
-    "#except ValueError:\n",
-    "#    print('Waring: Error in input MIC value')\n",
-    "#result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res,axis = 1)\n",
-    "#del result['CLSI_profile']"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 42,
-   "id": "7784b77d",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'input_user = sys.argv[1]\\ninput_clsi = sys.argv[2]\\noutput_table = sys.argv[3]'"
-      ]
-     },
-     "execution_count": 42,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "# for input argument\n",
-    "\"\"\"input_user = sys.argv[1]\n",
-    "input_clsi = sys.argv[2]\n",
-    "output_table = sys.argv[3]\"\"\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 43,
-   "id": "1dee9127",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "input_user='input.csv'\n",
-    "input_clsi='clsi.csv'\n",
-    "output_profile=input_user+'_profile.csv'\n",
-    "output_table=input_user+'_table.csv'"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "id": "14c5cfd3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# read user AST data with selected 3 columns\n",
-    "strain_mic=pd.read_csv(input_user, sep=',', usecols =['Strain name', 'Antibiotics', 'MIC'],na_filter=False)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "id": "77135cb7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "clsi_bp=pd.read_csv(input_clsi,sep=',')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 10,
-   "id": "2ec1cbec",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1\" class=\"dataframe\">\n",
-       "  <thead>\n",
-       "    <tr style=\"text-align: right;\">\n",
-       "      <th></th>\n",
-       "      <th>Antibiotics</th>\n",
-       "      <th>Susceptible</th>\n",
-       "      <th>Resistant</th>\n",
-       "      <th>Intermediate</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>Amikacin</td>\n",
-       "      <td>≤ 16</td>\n",
-       "      <td>≥ 64</td>\n",
-       "      <td>32</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>Tobramycin</td>\n",
-       "      <td>≤ 4</td>\n",
-       "      <td>≥ 16</td>\n",
-       "      <td>8</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>Gentamicin</td>\n",
-       "      <td>≤ 4</td>\n",
-       "      <td>≥ 16</td>\n",
-       "      <td>8</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>Netilmicin</td>\n",
-       "      <td>≤ 8</td>\n",
-       "      <td>≥ 32</td>\n",
-       "      <td>16</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>Imipenem</td>\n",
-       "      <td>≤ 2</td>\n",
-       "      <td>≥ 8</td>\n",
-       "      <td>4</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>5</th>\n",
-       "      <td>Meropenem</td>\n",
-       "      <td>≤ 2</td>\n",
-       "      <td>≥ 8</td>\n",
-       "      <td>4</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>6</th>\n",
-       "      <td>Doripenem</td>\n",
-       "      <td>≤ 2</td>\n",
-       "      <td>≥ 8</td>\n",
-       "      <td>4</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>7</th>\n",
-       "      <td>Ciprofloxacin</td>\n",
-       "      <td>≤ 1</td>\n",
-       "      <td>≥ 4</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>8</th>\n",
-       "      <td>Levofloxacin</td>\n",
-       "      <td>≤ 2</td>\n",
-       "      <td>≥ 8</td>\n",
-       "      <td>4</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>9</th>\n",
-       "      <td>Piperacillin/ tazobactam</td>\n",
-       "      <td>≤ 16/4</td>\n",
-       "      <td>≥ 128/4</td>\n",
-       "      <td>32/4-64/4</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>10</th>\n",
-       "      <td>Ticarcillin/ clavulanic acid</td>\n",
-       "      <td>≤ 16/2</td>\n",
-       "      <td>≥ 128/2</td>\n",
-       "      <td>32/2-64/2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>11</th>\n",
-       "      <td>Cefotaxime</td>\n",
-       "      <td>≤ 8</td>\n",
-       "      <td>≥ 64</td>\n",
-       "      <td>16-32</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>12</th>\n",
-       "      <td>Ceftriaxone</td>\n",
-       "      <td>≤ 8</td>\n",
-       "      <td>≥ 64</td>\n",
-       "      <td>16-32</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>13</th>\n",
-       "      <td>Ceftazidime</td>\n",
-       "      <td>≤ 8</td>\n",
-       "      <td>≥ 32</td>\n",
-       "      <td>16</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>14</th>\n",
-       "      <td>Cefepime</td>\n",
-       "      <td>≤ 8</td>\n",
-       "      <td>≥ 32</td>\n",
-       "      <td>16</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>15</th>\n",
-       "      <td>Trimethoprim/ sulfamethoxazole</td>\n",
-       "      <td>≤ 2/38</td>\n",
-       "      <td>≥ 4/76</td>\n",
-       "      <td>-</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>16</th>\n",
-       "      <td>Ampicillin/ sulbactam</td>\n",
-       "      <td>≤ 8/4</td>\n",
-       "      <td>≥ 32/16</td>\n",
-       "      <td>16/8</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>17</th>\n",
-       "      <td>Colistin</td>\n",
-       "      <td>-</td>\n",
-       "      <td>≥ 4</td>\n",
-       "      <td>≤ 2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>18</th>\n",
-       "      <td>Polymyxin B</td>\n",
-       "      <td>-</td>\n",
-       "      <td>≥ 4</td>\n",
-       "      <td>≤ 2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>19</th>\n",
-       "      <td>Tetracycline</td>\n",
-       "      <td>≤ 4</td>\n",
-       "      <td>≥ 16</td>\n",
-       "      <td>8</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>20</th>\n",
-       "      <td>Doxycycline</td>\n",
-       "      <td>≤ 4</td>\n",
-       "      <td>≥ 16</td>\n",
-       "      <td>8</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>21</th>\n",
-       "      <td>Minocycline</td>\n",
-       "      <td>≤ 4</td>\n",
-       "      <td>≥ 16</td>\n",
-       "      <td>8</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "                       Antibiotics Susceptible Resistant Intermediate\n",
-       "0                         Amikacin        ≤ 16      ≥ 64           32\n",
-       "1                       Tobramycin         ≤ 4      ≥ 16            8\n",
-       "2                       Gentamicin         ≤ 4      ≥ 16            8\n",
-       "3                       Netilmicin         ≤ 8      ≥ 32           16\n",
-       "4                         Imipenem         ≤ 2       ≥ 8            4\n",
-       "5                        Meropenem         ≤ 2       ≥ 8            4\n",
-       "6                        Doripenem         ≤ 2       ≥ 8            4\n",
-       "7                    Ciprofloxacin         ≤ 1       ≥ 4            2\n",
-       "8                     Levofloxacin         ≤ 2       ≥ 8            4\n",
-       "9         Piperacillin/ tazobactam      ≤ 16/4   ≥ 128/4    32/4-64/4\n",
-       "10    Ticarcillin/ clavulanic acid      ≤ 16/2   ≥ 128/2    32/2-64/2\n",
-       "11                      Cefotaxime         ≤ 8      ≥ 64        16-32\n",
-       "12                     Ceftriaxone         ≤ 8      ≥ 64        16-32\n",
-       "13                     Ceftazidime         ≤ 8      ≥ 32           16\n",
-       "14                        Cefepime         ≤ 8      ≥ 32           16\n",
-       "15  Trimethoprim/ sulfamethoxazole      ≤ 2/38    ≥ 4/76            -\n",
-       "16           Ampicillin/ sulbactam       ≤ 8/4   ≥ 32/16         16/8\n",
-       "17                        Colistin           -       ≥ 4          ≤ 2\n",
-       "18                     Polymyxin B           -       ≥ 4          ≤ 2\n",
-       "19                    Tetracycline         ≤ 4      ≥ 16            8\n",
-       "20                     Doxycycline         ≤ 4      ≥ 16            8\n",
-       "21                     Minocycline         ≤ 4      ≥ 16            8"
-      ]
-     },
-     "execution_count": 10,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "clsi_bp\n",
-    "#strain_mic"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 19,
-   "id": "860505f7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# convert MIC to numbers sMIC, rMIC\n",
-    "clsi_bp['s_mic'] =clsi_bp[['Susceptible']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n",
-    "clsi_bp['r_mic'] =clsi_bp[['Resistant']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n",
-    "clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 20,
-   "id": "cad964a6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 21,
-   "id": "2b6c02f5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Read only numbers in MIC values\n",
-    "#try:\n",
-    "strain_mic['o_mic']=strain_mic[['MIC']].applymap(lambda x: (re.sub(r'[^0-9.\\/]','', x)))\n",
-    "#except TypeError:\n",
-    "#    print('Waring: Error in MIC value')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 22,
-   "id": "942fefb2",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1\" class=\"dataframe\">\n",
-       "  <thead>\n",
-       "    <tr style=\"text-align: right;\">\n",
-       "      <th></th>\n",
-       "      <th>Strain name</th>\n",
-       "      <th>Antibiotics</th>\n",
-       "      <th>MIC</th>\n",
-       "      <th>o_mic</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>Acinetobacter baumannii A85</td>\n",
-       "      <td>Colistin</td>\n",
-       "      <td>0.1</td>\n",
-       "      <td>0.1</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>Acinetobacter baumannii A85</td>\n",
-       "      <td>Colistin</td>\n",
-       "      <td>1</td>\n",
-       "      <td>1</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>Acinetobacter baumannii A85</td>\n",
-       "      <td>Colistin</td>\n",
-       "      <td>2</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
-       "      <td>Ampicillin</td>\n",
-       "      <td>0</td>\n",
-       "      <td>0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
-       "      <td>Ampicillin/sulbactam</td>\n",
-       "      <td>mg/L</td>\n",
-       "      <td>/</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>5</th>\n",
-       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
-       "      <td>Piperacillin/tazobactam</td>\n",
-       "      <td>0</td>\n",
-       "      <td>0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>6</th>\n",
-       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
-       "      <td>Cefazolin</td>\n",
-       "      <td>64</td>\n",
-       "      <td>64</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>7</th>\n",
-       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
-       "      <td>Ceftriaxone</td>\n",
-       "      <td>16</td>\n",
-       "      <td>16</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>8</th>\n",
-       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
-       "      <td>Cefepime</td>\n",
-       "      <td>8</td>\n",
-       "      <td>8</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>9</th>\n",
-       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
-       "      <td>Meropenem</td>\n",
-       "      <td>0.25</td>\n",
-       "      <td>0.25</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>10</th>\n",
-       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
-       "      <td>Imipenem</td>\n",
-       "      <td>1</td>\n",
-       "      <td>1</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>11</th>\n",
-       "      <td>Acinetobacter baumannii AB307-0294</td>\n",
-       "      <td>Tigecycline</td>\n",
-       "      <td>0.5</td>\n",
-       "      <td>0.5</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>12</th>\n",
-       "      <td>Acinetobacter baumannii AB5075-UW</td>\n",
-       "      <td>Ceftazidime</td>\n",
-       "      <td>&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
-}
--- a/clsi_profile_type2_linux.ipynb	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,447 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 206,
-   "id": "967b1345",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics\n",
-    "# By rakesh4osdd@gmail.com, 06-Jun-2021\n",
-    "import pandas as pd\n",
-    "import re\n",
-    "import sys"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 207,
-   "id": "39e25c15",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#print(pd.__version__, re.__version__)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 208,
-   "id": "43115c0a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# compare two MIC value strings\n",
-    "def check_mic(mic1,mic2,mic_type):\n",
-    "    #print(mic1,mic2,mic_type)\n",
-    "    try:\n",
-    "        if '/' in mic1:\n",
-    "            m1a = mic1.split('/')[0]\n",
-    "            m1b = mic1.split('/')[1]\n",
-    "            if float(m1a)==0 or float(m1b)==0:\n",
-    "                strain_type='Strain could not be classified'\n",
-    "                return(strain_type)          \n",
-    "        elif '/' in mic2:\n",
-    "            m1a = mic1\n",
-    "            if float(m1a)==0:\n",
-    "                strain_type='Strain could not be classified'\n",
-    "                return(strain_type)            \n",
-    "            m1b = '1'\n",
-    "        elif float(mic1)==0:\n",
-    "            strain_type='Strain could not be classified'\n",
-    "            return(strain_type)\n",
-    "        else:\n",
-    "            m1a = mic1\n",
-    "            \n",
-    "        if '-' in mic2:\n",
-    "            m2a = mic2.split('-')[0]\n",
-    "            m2b = mic2.split('-')[1]           \n",
-    "         \n",
-    "    except ValueError:\n",
-    "        strain_type='Strain could not be classified' \n",
-    "        return(strain_type)\n",
-    "    try:\n",
-    "        if '-' in mic2 and mic_type == 'i':   # for intermediate only\n",
-    "            if '/' in mic2:\n",
-    "                m2a = mic2.split('-')[0].split('/')[0]\n",
-    "                m2b = mic2.split('-')[0].split('/')[1]\n",
-    "                m2aa = mic2.split('-')[1].split('/')[0]\n",
-    "                m2bb = mic2.split('-')[1].split('/')[1]\n",
-    "                if (float(m2aa)>=float(m1a)>=float(m2a) and float(m2bb)>=float(m1b)>=float(m2b)):\n",
-    "                    #print('intermediate')\n",
-    "                    m_type='Intermediate'\n",
-    "                else:\n",
-    "                    #print('not define')\n",
-    "                    m_type='Strain could not be classified'\n",
-    "            else:\n",
-    "                m2a = mic2.split('-')[0]\n",
-    "                m2b = mic2.split('-')[1] \n",
-    "                if (float(m2b)>=float(m1a)>=float(m2a)):\n",
-    "                    #print('intermediate')\n",
-    "                    m_type='Intermediate'\n",
-    "                else:\n",
-    "                    #print('not define')\n",
-    "                    m_type='Strain could not be classified'                \n",
-    "            #print (m1a,m1b,m2a,m2b,m2aa,m2bb)\n",
-    "        elif '/' in mic2:\n",
-    "            m2a = mic2.split('/')[0]\n",
-    "            m2b = mic2.split('/')[1]\n",
-    "            #print(m1a,m1b,m2a,m2b,mic_type)\n",
-    "            if (mic_type=='s' and (float(m1a)<=float(m2a) and float(m1b)<=float(m2b))):\n",
-    "                m_type='Susceptible'\n",
-    "            elif (mic_type=='r' and (float(m1a)>=float(m2a) and float(m1b)>=float(m2b))):\n",
-    "                m_type='Resistant'\n",
-    "            elif (mic_type=='i' and (float(m1a)==float(m2a) and float(m1b)==float(m2b))):\n",
-    "                m_type='Intermediate'\n",
-    "            else:\n",
-    "                m_type='Strain could not be classified'\n",
-    "        elif '-' in mic2:\n",
-    "                m_type='Strain could not be classified'\n",
-    "        else:\n",
-    "            m2a=mic2\n",
-    "            if (mic_type=='s' and (float(m1a)<=float(m2a))):\n",
-    "                m_type='Susceptible'\n",
-    "            elif (mic_type=='r' and (float(m1a)>=float(m2a))):\n",
-    "                m_type='Resistant'\n",
-    "            elif (mic_type=='i' and (float(m1a)==float(m2a))):\n",
-    "                m_type='Intermediate'\n",
-    "            else:\n",
-    "                m_type='Strain could not be classified-1'        \n",
-    "    except IndexError:\n",
-    "        strain_type='Strain could not be classified-2' \n",
-    "        return(strain_type)\n",
-    "    \n",
-    "    return(m_type)\n",
-    "\n",
-    "#check_mic('65','32-64','i')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 209,
-   "id": "0448ebf3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# compare MIC value in pandas list\n",
-    "def sus_res_int(mic):\n",
-    "    #print(mic)\n",
-    "    o_mic = mic[0].replace(' ', '')\n",
-    "    s_mic = mic[1].replace(' ', '')\n",
-    "    r_mic = mic[2].replace(' ', '')\n",
-    "    i_mic = mic[3].replace(' ', '')\n",
-    "    try:\n",
-    "        if check_mic(o_mic,s_mic,'s')=='Susceptible':\n",
-    "            strain_type='Susceptible'\n",
-    "        elif check_mic(o_mic,r_mic,'r')=='Resistant':\n",
-    "            strain_type='Resistant'\n",
-    "        elif check_mic(o_mic,i_mic,'i')=='Intermediate':\n",
-    "            strain_type='Intermediate'                    \n",
-    "        else:\n",
-    "            strain_type='Strain could not be classified'\n",
-    "    except ValueError:\n",
-    "        strain_type='Strain could not be classified'            \n",
-    "    return(strain_type)\n",
-    "\n",
-    "#mic=['128','16/4','128/4','32/4-64/4']\n",
-    "#sus_res_int(mic)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 210,
-   "id": "7784b77d",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'input_user = sys.argv[1]\\ninput_clsi = sys.argv[2]\\noutput_table = sys.argv[3]'"
-      ]
-     },
-     "execution_count": 210,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "# for input argument\n",
-    "\"\"\"input_user = sys.argv[1]\n",
-    "input_clsi = sys.argv[2]\n",
-    "output_table = sys.argv[3]\"\"\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 211,
-   "id": "1dee9127",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "input_user='input.csv'\n",
-    "input_clsi='clsi.csv'\n",
-    "output_profile=input_user+'_profile.csv'\n",
-    "output_table=input_user+'_table.csv'"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 212,
-   "id": "14c5cfd3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# read user AST data with selected 3 columns\n",
-    "strain_mic=pd.read_csv(input_user, sep=',', usecols =['Strain name', 'Antibiotics', 'MIC'],na_filter=False)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 213,
-   "id": "77135cb7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "clsi_bp=pd.read_csv(input_clsi,sep=',')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 214,
-   "id": "2ec1cbec",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#clsi_bp\n",
-    "#strain_mic"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 215,
-   "id": "860505f7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# convert MIC to numbers sMIC, rMIC\n",
-    "clsi_bp['s_mic'] =clsi_bp[['Susceptible']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n",
-    "clsi_bp['r_mic'] =clsi_bp[['Resistant']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n",
-    "clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 216,
-   "id": "3eee0538",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 217,
-   "id": "2b6c02f5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Read only numbers in MIC values\n",
-    "#try:\n",
-    "strain_mic['o_mic']=strain_mic[['MIC']].applymap(lambda x: (re.sub(r'[^0-9.\\/]','', x)))\n",
-    "#except TypeError:\n",
-    "#    print('Waring: Error in MIC value')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 218,
-   "id": "942fefb2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#strain_mic"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 219,
-   "id": "bba6b0a2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# capitalize each Antibiotic Name for comparision with removing whitespace\n",
-    "strain_mic['Antibiotics']=strain_mic['Antibiotics'].str.capitalize().str.replace(\" \",\"\")\n",
-    "clsi_bp['Antibiotics']=clsi_bp['Antibiotics'].str.capitalize().str.replace(\" \",\"\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 220,
-   "id": "ea403928",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#compare CLSI Antibiotics only\n",
-    "#result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner',  indicator=True)[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','_merge']]\n",
-    "try:\n",
-    "    result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner')[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','i_mic']]\n",
-    "except KeyError:\n",
-    "    print('Waring: Error in input Values')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 221,
-   "id": "44f7e35d",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#compare MIC values and assign Susceptible and Resistant to Strain\n",
-    "#try:\n",
-    "result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res_int,axis = 1)\n",
-    "#except ValueError:\n",
-    "#    print('Waring: Error in input MIC value')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 222,
-   "id": "30c2a7a3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#result"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 223,
-   "id": "ab7d8379",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#result[['Strain name', 'Antibiotics', 'MIC','s_mic','r_mic','CLSI_profile']].to_csv(output_profile,sep=',', index=False, encoding='utf-8-sig')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 224,
-   "id": "a426ae2b",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#create a pivot table for ASIST\n",
-    "table=result[['Strain name', 'Antibiotics','CLSI_profile']].drop_duplicates()\n",
-    "result_table=pd.pivot_table(table, values ='CLSI_profile', index =['Strain name'],columns =['Antibiotics'], aggfunc = lambda x: ' '.join(x))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 225,
-   "id": "df439a58",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#result_table"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 226,
-   "id": "ee19e872",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#result_table.to_csv(output_table,na_rep='NA')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 227,
-   "id": "692ab948",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# reorder the Antibiotics for ASIST\n",
-    "clsi_ab=['Amikacin','Tobramycin','Gentamycin','Imipenem','Meropenem','Doripenem','Ciprofloxacin','Levofloxacin',\n",
-    "         'Piperacillin/tazobactam','Ticarcillin/clavulanicacid','Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime',\n",
-    "         'Trimethoprim/sulfamethoxazole','Ampicillin/sulbactam','Colistin','Polymyxinb','Tetracycline','Doxicycline ',\n",
-    "         'Minocycline']\n",
-    "result_selected=result_table.filter(clsi_ab)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 228,
-   "id": "e0d983b9",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#print(result_selected.shape, result_table.shape)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 229,
-   "id": "1b0a4d77",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "result_selected.insert(0,'Resistance_phenotype','')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 230,
-   "id": "5c162c07",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#rename headers\n",
-    "result_selected=result_selected.rename(columns = {'Ticarcillin/clavulanicacid':'Ticarcillin/clavulanic acid','Piperacillin/tazobactam':'Piperacillin/ tazobactam','Trimethoprim/sulfamethoxazole': 'Trimethoprim/ sulfamethoxazole','Ampicillin/sulbactam':'Ampicillin/ sulbactam', 'Polymyxinb': 'Polymyxin B'} )"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 231,
-   "id": "00cd53d4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#result_selected"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 232,
-   "id": "d36dcdab",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "result_selected.to_csv(output_table,na_rep='NA')"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.1"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
--- a/dump/clsi.csv	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-Antibiotics,Susceptible,Resistant
-Amikacin,≤ 16,≥ 64
-Tobramycin,≤ 4,≥ 16
-Gentamicin,≤ 4,≥ 16
-Netilmicin,≤ 8,≥ 32
-Imipenem,≤ 2,≥ 8
-Meropenem,≤ 2,≥ 8
-Doripenem,≤ 2,≥ 8
-Ciprofloxacin,≤ 1,≥ 4
-Levofloxacin,≤ 2,≥ 8
-Piperacillin/ tazobactam,≤ 16/4,≥ 128/4
-Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2
-Cefotaxime,≤ 8,≥ 64
-Ceftriaxone,≤ 8,≥ 64
-Ceftazidime,≤ 8,≥ 32
-Cefepime,≤ 8,≥ 32
-Trimethoprim/ sulfamethoxazole,≤ 2/38,≥ 4/76
-Ampicillin/ sulbactam,≤ 8/4,≥ 32/16
-Colistin,≤ 2,≥ 4
-Polymyxin B,≤ 2,≥ 4
-Tetracycline,≤ 4,≥ 16
-Doxycycline,≤ 4,≥ 16
-Minocycline,≤ 4,≥ 16
\ No newline at end of file
--- a/dump/clsi_profile.xml	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-<tool id="clsi_profile" name="CLSI Profile" version="0.1.0" python_template_version="3.5">
-    <description>MIC profile using CLSI MIC breakpoints</description>
-
-    <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/clsi_profile.py' '$input1' '$input2' '$output1'
-    ]]></command>
-    <inputs>
-        <param type="data" name="input1" format="csv" />
-        <param type="data" name="input2" format="csv" />
-    </inputs>
-    <outputs>
-        <data name="output1" format="csv" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" value="input.csv"/>
-            <param name="input2" value="clsi.csv"/>
-            <output name="output1" file="output.csv"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-        Examples Files:
-	    **CLSI MIC breakpoint file example:** ::
-
-	    Antibiotics,Susceptible,Resistant,Intermediate
-	    Amikacin,≤ 16,≥ 64,32
-	    Tobramycin,≤ 4,≥ 16,8
-	    Gentamicin,≤ 4,≥ 16,8
-
-	    **AST MIC value file example:** ::
-            Strain name,Antibiotics,MIC
-	    Strain1,Amikacin,≤ 16
-	    Strain2,Tobramycin,≤ 4
-	    Strain3,Gentamicin,≤ 4
-    ]]></help>
-</tool>
--- a/dump/clsi_profile_comb.csv	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-Antibiotics,Susceptible,Resistant
-Amikacin,≤ 16,≥ 64
-Tobramycin,≤ 4,≥ 16
-Gentamicin,≤ 4,≥ 16
-Netilmicin,≤ 8,≥ 32
-Imipenem,≤ 2,≥ 8
-Meropenem,≤ 2,≥ 8
-Doripenem,≤ 2,≥ 8
-Ciprofloxacin,≤ 1,≥ 4
-Levofloxacin,≤ 2,≥ 8
-Piperacillin/ tazobactam,≤ 16/4,≥ 128/4
-Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2
-Cefotaxime,≤ 8,≥ 64
-Ceftriaxone,≤ 8,≥ 64
-Ceftazidime,≤ 8,≥ 32
-Cefepime,≤ 8,≥ 32
-Trimethoprim/ sulfamethoxazole,≤ 2/38,≥ 4/76
-Ampicillin/ sulbactam,≤ 8/4,≥ 32/16
-Colistin,≤ 2,≥ 4
-Polymyxin B,≤ 2,≥ 4
-Tetracycline,≤ 4,≥ 16
-Doxycycline,≤ 4,≥ 16
-Minocycline,≤ 4,≥ 16
\ No newline at end of file
--- a/dump/input.csv	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-id,genome Ids,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,1,mg/L
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,2,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
-470,CP015483.1,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L
-470,470.7601,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7651,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7764,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.8071,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7405,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L
-470,470.7406,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L
-470,470.7407,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L
-470,470.7408,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
--- a/dump/input_ast_comb2.csv	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-id,genome Ids,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,1,mg/L
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,2,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
-470,CP015483.1,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L
-470,470.7601,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7651,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7764,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.8071,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7405,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L
-470,470.7406,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L
-470,470.7407,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L
-470,470.7408,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
--- a/dump/input_ast_comb2.csv_table.csv	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-Strain name,Resistance_phenotype,Imipenem,Meropenem,Ciprofloxacin,Piperacillin/tazobactam,Ticarcillin/clavulanicacid,Ceftriaxone,Ceftazidime,Cefepime,Trimethoprim/sulfamethoxazole,Ampicillin/sulbactam,Colistin,Polymyxinb
-Acinetobacter baumannii A85,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible,NA
-Acinetobacter baumannii AB307-0294,,Susceptible,Susceptible,NA,Strain could not classified,NA,Intermediate,NA,Susceptible,NA,Strain could not classified,NA,NA
-Acinetobacter baumannii AB5075-UW,,NA,NA,Resistant,NA,NA,NA,Resistant,Resistant,NA,NA,NA,NA
-Acinetobacter baumannii DU202,,NA,NA,NA,Strain could not classified,Resistant,NA,NA,NA,Resistant,Strain could not classified,Strain could not classified,NA
-Acinetobacter baumannii ORAB01,,NA,NA,NA,Intermediate,NA,NA,NA,NA,NA,NA,NA,NA
-Acinetobacter baumannii strain FDA-CDC-AR_0305,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible
-Acinetobacter baumannii strain FDA-CDC-AR_0306,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible
-Acinetobacter baumannii strain FDA-CDC-AR_0307,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant
-Acinetobacter baumannii strain FDA-CDC-AR_0308,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant
--- a/dump/output.csv	Fri Jun 11 12:36:25 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-Strain name,Resistance_phenotype,Imipenem,Meropenem,Ciprofloxacin,Piperacillin/tazobactam,Ticarcillin/clavulanicacid,Ceftriaxone,Ceftazidime,Cefepime,Trimethoprim/sulfamethoxazole,Ampicillin/sulbactam,Colistin,Polymyxinb
-Acinetobacter baumannii A85,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible,NA
-Acinetobacter baumannii AB307-0294,,Susceptible,Susceptible,NA,Strain could not classified,NA,Intermediate,NA,Susceptible,NA,Strain could not classified,NA,NA
-Acinetobacter baumannii AB5075-UW,,NA,NA,Resistant,NA,NA,NA,Resistant,Resistant,NA,NA,NA,NA
-Acinetobacter baumannii DU202,,NA,NA,NA,Strain could not classified,Resistant,NA,NA,NA,Resistant,Strain could not classified,Strain could not classified,NA
-Acinetobacter baumannii ORAB01,,NA,NA,NA,Intermediate,NA,NA,NA,NA,NA,NA,NA,NA
-Acinetobacter baumannii strain FDA-CDC-AR_0305,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible
-Acinetobacter baumannii strain FDA-CDC-AR_0306,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible
-Acinetobacter baumannii strain FDA-CDC-AR_0307,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant
-Acinetobacter baumannii strain FDA-CDC-AR_0308,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant