Mercurial > repos > rakesh4osdd > clsi_profile
annotate clsi_profile.py @ 11:7dcc0e93288b draft default tip
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
author | rakesh4osdd |
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date | Wed, 30 Jun 2021 07:13:29 +0000 |
parents | 3c27e5c2a8e9 |
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0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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1 #!/usr/bin/env python |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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2 # coding: utf-8 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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3 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
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4
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4 # In[7]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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5 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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6 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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7 # ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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8 # By rakesh4osdd@gmail.com, 06-Jun-2021 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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9 import pandas as pd |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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10 import re |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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11 import sys |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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12 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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13 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
4
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14 # In[8]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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15 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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16 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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17 #print(pd.__version__, re.__version__) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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18 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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19 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
4
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20 # In[9]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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21 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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22 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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23 # compare two MIC value strings |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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24 def check_mic(mic1,mic2,mic_type): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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25 #print(mic1,mic2,mic_type) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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26 try: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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27 if '/' in mic1: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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28 m1a = mic1.split('/')[0] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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29 m1b = mic1.split('/')[1] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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30 if float(m1a)==0 or float(m1b)==0: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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31 strain_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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32 return(strain_type) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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33 elif '/' in mic2: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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34 m1a = mic1 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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35 if float(m1a)==0: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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36 strain_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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37 return(strain_type) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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38 m1b = '1' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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39 elif float(mic1)==0: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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40 strain_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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41 return(strain_type) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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42 else: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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43 m1a = mic1 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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44 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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45 if '-' in mic2: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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46 m2a = mic2.split('-')[0] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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47 m2b = mic2.split('-')[1] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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48 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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49 except ValueError: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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50 strain_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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51 return(strain_type) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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52 try: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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53 if '-' in mic2 and mic_type == 'i': # for intermediate only |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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54 if '/' in mic2: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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55 m2a = mic2.split('-')[0].split('/')[0] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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56 m2b = mic2.split('-')[0].split('/')[1] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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57 m2aa = mic2.split('-')[1].split('/')[0] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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58 m2bb = mic2.split('-')[1].split('/')[1] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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59 if (float(m2aa)>=float(m1a)>=float(m2a) and float(m2bb)>=float(m1b)>=float(m2b)): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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60 #print('intermediate') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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61 m_type='Intermediate' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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62 else: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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63 #print('not define') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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64 m_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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65 else: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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66 m2a = mic2.split('-')[0] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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67 m2b = mic2.split('-')[1] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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68 if (float(m2b)>=float(m1a)>=float(m2a)): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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69 #print('intermediate') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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70 m_type='Intermediate' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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71 else: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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72 #print('not define') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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73 m_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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74 #print (m1a,m1b,m2a,m2b,m2aa,m2bb) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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75 elif '/' in mic2: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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76 m2a = mic2.split('/')[0] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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77 m2b = mic2.split('/')[1] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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78 #print(m1a,m1b,m2a,m2b,mic_type) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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79 if (mic_type=='s' and (float(m1a)<=float(m2a) and float(m1b)<=float(m2b))): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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80 m_type='Susceptible' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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81 elif (mic_type=='r' and (float(m1a)>=float(m2a) and float(m1b)>=float(m2b))): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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82 m_type='Resistant' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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83 elif (mic_type=='i' and (float(m1a)==float(m2a) and float(m1b)==float(m2b))): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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84 m_type='Intermediate' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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parents:
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85 else: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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86 m_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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87 elif '-' in mic2: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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88 m_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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89 else: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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90 m2a=mic2 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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91 if (mic_type=='s' and (float(m1a)<=float(m2a))): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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92 m_type='Susceptible' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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93 elif (mic_type=='r' and (float(m1a)>=float(m2a))): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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94 m_type='Resistant' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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95 elif (mic_type=='i' and (float(m1a)==float(m2a))): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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96 m_type='Intermediate' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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parents:
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97 else: |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
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98 m_type='Strain could not be classified' |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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parents:
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99 except IndexError: |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
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100 strain_type='Strain could not be classified' |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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101 return(strain_type) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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102 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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103 return(m_type) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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104 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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105 #check_mic('65','32-64','i') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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106 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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107 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
4
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|
108 # In[10]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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parents:
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109 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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110 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
111 # compare MIC value in pandas list |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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112 def sus_res_int(mic): |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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113 #print(mic) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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114 o_mic = mic[0].replace(' ', '') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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115 s_mic = mic[1].replace(' ', '') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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116 r_mic = mic[2].replace(' ', '') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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117 i_mic = mic[3].replace(' ', '') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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118 try: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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119 if check_mic(o_mic,s_mic,'s')=='Susceptible': |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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120 strain_type='Susceptible' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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121 elif check_mic(o_mic,r_mic,'r')=='Resistant': |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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122 strain_type='Resistant' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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123 elif check_mic(o_mic,i_mic,'i')=='Intermediate': |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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124 strain_type='Intermediate' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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125 else: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
126 strain_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
127 except ValueError: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
128 strain_type='Strain could not be classified' |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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129 return(strain_type) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
130 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
131 #mic=['128','16/4','128/4','32/4-64/4'] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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132 #sus_res_int(mic) |
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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133 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
134 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
4
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|
135 # In[11]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
136 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
137 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
138 # for input argument |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
139 input_user = sys.argv[1] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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140 input_clsi = sys.argv[2] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
141 output_table = sys.argv[3] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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142 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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|
143 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
4
diff
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|
144 # In[49]: |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
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3
diff
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|
145 |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
146 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
4
diff
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|
147 """input_user='~/Jupyterlab_notebook/ASIST_module/strain_profiles_16k.csv.csv' |
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
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|
148 #input_user='test-data/input2.csv' |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
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|
149 input_clsi='test-data/clsi.csv' |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
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|
150 output_profile='test-data/input2_profile.csv' |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
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|
151 #output_table='test-data/input2_table.csv' |
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
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|
152 output_table='/home/rakesh/Jupyterlab_notebook/ASIST_module/strain_profiles_16k_table.csv'""" |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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|
153 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
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|
154 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
4
diff
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|
155 # In[60]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
156 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
157 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
158 # read user AST data with selected 3 columns |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
159 strain_mic=pd.read_csv(input_user, sep=',', usecols =['Strain name', 'Antibiotics', 'MIC'],na_filter=False) |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
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|
160 #strain_mic |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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|
161 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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162 |
5
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
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163 # In[61]: |
0
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164 |
62226cd1acb5
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165 |
62226cd1acb5
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166 clsi_bp=pd.read_csv(input_clsi,sep=',') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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167 |
4
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168 #clsi_bp[clsi_bp[['Antibiotics', 'Susceptible']].duplicated()].shape |
0
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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169 |
4
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170 |
5
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
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171 # In[62]: |
0
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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172 |
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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173 |
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174 #clsi_bp |
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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175 #strain_mic |
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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176 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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177 |
5
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
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178 # In[64]: |
4
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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179 |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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180 |
5
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
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181 # warn user for duplicate files |
4
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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182 input_dups=strain_mic[strain_mic[['Strain name','Antibiotics']].duplicated()] |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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183 if (input_dups.shape[0] == 0): |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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184 #print( "No duplicates") |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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185 pass |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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186 else: |
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187 with open(output_table, "w") as file_object: |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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188 # Append 'hello' at the end of file |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
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189 file_object.write('S.No.,Strain name,Antibiotics,MIC\nInput File Error: Please remove duplicate/mutiple MIC values for same combination of Strain name and Antibiotics from input file\n') |
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
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190 input_dups.to_csv(output_table,na_rep='NA', mode='a') |
4
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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191 exit() |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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192 |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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193 |
5
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
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194 # In[17]: |
0
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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195 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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196 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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197 # convert MIC to numbers sMIC, rMIC |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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198 clsi_bp['s_mic'] =clsi_bp[['Susceptible']].applymap(lambda x: (re.sub(r'[^0-9.\/-]', '', x))) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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199 clsi_bp['r_mic'] =clsi_bp[['Resistant']].applymap(lambda x: (re.sub(r'[^0-9.\/-]', '', x))) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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200 clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\/-]', '', x))) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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201 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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202 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
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203 # In[18]: |
0
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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204 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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205 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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206 #clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\/-]', '', x))) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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207 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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208 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
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209 # In[19]: |
0
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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210 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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211 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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212 # Read only numbers in MIC values |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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213 #try: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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214 strain_mic['o_mic']=strain_mic[['MIC']].applymap(lambda x: (re.sub(r'[^0-9.\/]','', x))) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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215 #except TypeError: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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216 # print('Waring: Error in MIC value') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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217 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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218 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
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219 # In[20]: |
0
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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220 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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221 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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222 #strain_mic |
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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223 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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224 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
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225 # In[21]: |
0
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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226 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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227 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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228 # capitalize each Antibiotic Name for comparision with removing whitespace |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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229 strain_mic['Strain name']=strain_mic['Strain name'].str.capitalize().str.replace(" ","") |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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230 strain_mic['Antibiotics']=strain_mic['Antibiotics'].str.capitalize().str.replace(" ","") |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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231 |
0
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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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232 clsi_bp['Antibiotics']=clsi_bp['Antibiotics'].str.capitalize().str.replace(" ","") |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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233 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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234 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
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235 # In[22]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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236 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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237 |
4
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
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238 #find duplicate values in input files |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
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239 dups=strain_mic[strain_mic[['Strain name', 'Antibiotics']].duplicated(keep=False)] |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
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240 if dups.shape[0] != 0: |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
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241 print ('Please provide a single MIC value in input file for given duplicates combination of \'Strain name and Antibiotics\' to use the tool:-\n',dups) |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
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242 #exit() |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
243 else: |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
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244 #compare CLSI Antibiotics only |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
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245 #result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner', indicator=True)[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','_merge']] |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
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246 try: |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
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247 result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner')[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','i_mic']] |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
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248 except KeyError: |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
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249 print('Waring: Error in input Values') |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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250 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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251 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
4
diff
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|
252 # In[23]: |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
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253 |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
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|
254 |
5
3c27e5c2a8e9
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
rakesh4osdd
parents:
4
diff
changeset
|
255 dups.head() |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
256 |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
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257 |
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
258 # In[132]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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259 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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260 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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|
261 #compare MIC values and assign Susceptible and Resistant to Strain |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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262 #try: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
263 result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res_int,axis = 1) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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264 #except ValueError: |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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265 # print('Waring: Error in input MIC value') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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|
266 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
267 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
268 # In[133]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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|
269 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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|
270 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
271 #result |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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|
272 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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|
273 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
274 # In[134]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
275 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
276 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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|
277 #result[['Strain name', 'Antibiotics', 'MIC','s_mic','r_mic','CLSI_profile']].to_csv(output_profile,sep=',', index=False, encoding='utf-8-sig') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
278 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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|
279 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
280 # In[135]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
281 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
282 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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|
283 #create a pivot table for ASIST |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
284 table=result[['Strain name', 'Antibiotics','CLSI_profile']].drop_duplicates() |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
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|
285 result_table=pd.pivot_table(table, values ='CLSI_profile', index =['Strain name'],columns =['Antibiotics'], aggfunc = lambda x: ' '.join(x)) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
286 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
287 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
288 # In[136]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
289 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
290 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
291 #result_table |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
292 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
293 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
294 # In[137]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
295 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
296 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
297 #result_table.to_csv(output_table,na_rep='NA') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
298 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
299 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
300 # In[138]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
301 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
302 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
303 # reorder the Antibiotics for ASIST |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
304 clsi_ab=['Amikacin','Tobramycin','Gentamycin','Netilmicin','Imipenem','Meropenem','Doripenem','Ciprofloxacin','Levofloxacin', |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
305 'Piperacillin/tazobactam','Ticarcillin/clavulanicacid','Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime', |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
306 'Trimethoprim/sulfamethoxazole','Ampicillin/sulbactam','Colistin','Polymyxinb','Tetracycline','Doxicycline ', |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
307 'Minocycline'] |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
308 result_selected=result_table.filter(clsi_ab) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
309 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
310 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
311 # In[139]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
312 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
313 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
314 #print(result_selected.shape, result_table.shape) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
315 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
316 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
317 # In[140]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
318 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
319 |
3
683299422575
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents:
0
diff
changeset
|
320 #result_selected.insert(0,'Resistance_phenotype','') |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
321 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
322 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
changeset
|
323 # In[141]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff
changeset
|
324 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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325 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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326 #rename headers |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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327 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'} ) |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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328 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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329 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
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330 # In[142]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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331 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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332 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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333 #result_selected |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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334 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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335 |
4
2a5861818faf
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
3
diff
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336 # In[144]: |
0
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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337 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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338 |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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339 result_selected.to_csv(output_table,na_rep='NA') |
62226cd1acb5
"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
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340 |