Mercurial > repos > rakesh4osdd > clsi_profile

annotate asist_dynamic.py @ 9:b3c01b790314 draft

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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
author rakesh4osdd
date Wed, 30 Jun 2021 06:37:12 +0000
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9
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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1 #!/usr/bin/env python
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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2 # coding: utf-8
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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4 # In[1309]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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7 #ASIST program for phenotype based on Antibiotics profile
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8 # create a profile based on selected antibiotics only
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9 # rakesh4osdd@gmail.com, 14-June-2021
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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12 # In[1]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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13
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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15 import pandas as pd
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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16 import sys
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17 import os
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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18 from collections import Counter
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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21 # In[176]:
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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24 input_file=sys.argv[1]
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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25 output_file=sys.argv[2]
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26 #input_file='test-data/asist_input.csv'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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27 #output_file='test-data/asist_output.csv'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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30 # In[177]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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33 # strain_profile to phenotype condition
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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34 def s_phen(sus,res,intm,na,pb_sus):
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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35 if (sus>0 and res==0 and na>=0):
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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36 #print('Possible Susceptible')
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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37 phen='Possible Susceptible'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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38 elif (sus>=0 and 3<=res<7 and na>=0 and pb_sus==0):
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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39 #print('Possible MDR')
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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40 phen='Possible MDR'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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41 elif (sus>=0 and 7<=res<9 and na>=0 and pb_sus==0):
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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42 #print('Possible XDR')
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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43 phen='Possible XDR'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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44 #special cases
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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45 elif (sus>=1 and res>0 and na>=0 and pb_sus==1):
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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46 #print('Possible XDR')
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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47 phen='Possible XDR'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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48 #special cases
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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49 elif (sus>0 and res==9 and na>=0):
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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50 #print('Possible XDR')
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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51 phen='Possible XDR'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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52 elif (sus==0 and res==9 and na>=0):
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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53 #print('Possible TDR')
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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54 phen='Possible TDR'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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55 else:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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56 #print('Strain could not be classified')
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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57 phen='Strain could not be classified ('+ str(intm)+' | ' + str(na) +')'
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58 return(phen)
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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60 #print(s_phen(1,9,0,0))
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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63 # In[178]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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66 # define Antibiotic groups as per antibiotic of CLSI breakpoints MIC
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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67 #Aminoglycoside
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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68 cat1=['Amikacin','Tobramycin','Gentamycin','Netilmicin']
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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69 #Beta-lactams- Carbapenems
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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70 cat2=['Imipenem','Meropenam','Doripenem']
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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71 #Fluoroquinolone
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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72 cat3=['Ciprofloxacin','Levofloxacin']
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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73 #Beta-lactam inhibitor
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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74 cat4=['Piperacillin/tazobactam','Ticarcillin/clavulanicacid']
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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75 #Cephalosporin
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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76 cat5=['Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime']
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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77 #Sulfonamides
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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78 cat6=['Trimethoprim/sulfamethoxazole']
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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79 #Penicillins/beta-lactamase
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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80 cat7=['Ampicillin/sulbactam']
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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81 #Polymyxins
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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82 cat8=['Colistin','Polymyxinb']
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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83 #Tetracycline
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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84 cat9=['Tetracycline','Doxicycline','Minocycline']
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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85
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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86 def s_profiler(pd_series):
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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87 #print(type(pd_series),'\n', pd_series)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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88 #create a dictionary of dataframe series
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
89 cats={'s1':cat1,'s2':cat2,'s3':cat3,'s4':cat4,'s5':cat5,'s6':cat6,'s7':cat7,'s8':cat8,'s9':cat9}
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
90 # find the antibiotics name in input series
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
91 for cat in cats:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
92 #print(cats[cat])
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
93 cats[cat]=pd_series.filter(cats[cat])
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
94 #print(cats[cat])
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
95 #define res,sus,intm,na,pb_sus
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
96 res=0
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
97 sus=0
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
98 intm=0
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
99 na=0
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
100 pb_sus=0
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
101 # special case of 'Polymyxin b' for its value
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
102 if 'Polymyxinb' in pd_series:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
103 ctp=cats['s8']['Polymyxinb'].strip().lower()
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
104 if ctp == 'susceptible':
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
105 pb_sus=1
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
106 #print((ctp,p_sus))
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
107 # check all categories
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
108 for cat in cats:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
109 #ctp=cats['s8'].iloc[i:i+1].stack().value_counts().to_dict()
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
110 #print(ctp)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
111 # Pandas series
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
112 ct=cats[cat].value_counts().to_dict()
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
113 #print(ct)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
114 # remove whitespace and convert to lowercase words
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
115 ct = {k.strip().lower(): v for k, v in ct.items()}
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
116 #print(ct)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
117 k=Counter(ct)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
118 #j=Counter(ct)+Counter(j)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
119 #print(j)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
120 # category wise marking
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
121 if k['resistant']>=1:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
122 res=res+1
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
123 if k['susceptible']>=1:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
124 sus=sus+1
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
125 if k['intermediate']>=1:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
126 intm=intm+1
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
127 if k['na']>=1:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
128 na=na+1
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
129 #print(sus,res,intm,na,pb_sus)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
130 #print(s_phen(sus,res,intm,na,pb_sus))
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
131 return(s_phen(sus,res,intm,na,pb_sus))
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
132
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
133
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
134 # In[179]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
135
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
136
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
137 #input_file='input2.csv_table.csv'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
138 #output_file=input_file+'_output.txt'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
139 strain_profile=pd.read_csv(input_file, sep=',',na_filter=False,skipinitialspace = True)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
140
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
141
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
142 # In[180]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
143
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
144
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
145 old_strain_name=strain_profile.columns[0]
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
146 new_strain_name=old_strain_name.capitalize().strip().replace(' ', '')
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
147
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
148
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
149 # In[181]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
150
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
151
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
152 # make header capitalization, remove leading,lagging, and multiple whitespace for comparision
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
153 strain_profile.columns=strain_profile.columns.str.capitalize().str.strip().str.replace('\s+', '', regex=True)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
154 #print(strain_profile.columns)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
155 #strain_profile.head()
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
156 #strain_profile.columns
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
157
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
158
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
159 # In[182]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
160
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
161
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
162 # add new column in dataframe on second position
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
163 strain_profile.insert(1, 'Strain phenotype','')
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
164 #strain_profile.head()
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
165
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
166
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
167 # In[183]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
168
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
169
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
170 strain_profile['Strain phenotype'] = strain_profile.apply(lambda x: (s_profiler(x)), axis=1)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
171
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
172
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
173 # In[184]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
174
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
175
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
176 #strain_profile.head()
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
diff changeset
177
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
parents:
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178
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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179 # In[185]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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180
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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181
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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182 #rename headers for old name
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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183 strain_profile=strain_profile.rename(columns = {new_strain_name:old_strain_name, 'Ticarcillin/clavulanicacid':'Ticarcillin/ clavulanic acid','Piperacillin/tazobactam':'Piperacillin/ tazobactam','Trimethoprim/sulfamethoxazole': 'Trimethoprim/ sulfamethoxazole','Ampicillin/sulbactam':'Ampicillin/ sulbactam', 'Polymyxinb': 'Polymyxin B'} )
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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184
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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185
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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186 # In[186]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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187
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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188
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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189 #strain_profile.columns
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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190
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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191
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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192 # In[187]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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193
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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194
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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195 #strain_profile
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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196
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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197
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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198 # In[188]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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199
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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200
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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201 strain_profile.to_csv(output_file,na_rep='NA',index=False)
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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202
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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203
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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204 # In[189]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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205
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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206
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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207 # Open a file with access mode 'a'
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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208 with open(output_file, "a") as file_object:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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209 # Append 'hello' at the end of file
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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210 file_object.write("Note: \n1. 'MDR': Multidrug-resistant, 'XDR': Extensively drug-resistant, 'TDR':totally drug resistant, NA': Data Not Available.\n2. 'Strain could not be classified' numbers follow the format as ('Number of antibiotics categories count as Intermediate' | 'Number of antibiotics categories count as NA')")
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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211
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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212
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
rakesh4osdd
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213 # In[ ]:
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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214
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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215
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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216
b3c01b790314 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8"
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217