Mercurial > repos > rakesh4osdd > clsi_profile
annotate clsi_profile_type2_linux.ipynb @ 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 |
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rev | line source |
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11
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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1 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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2 "cells": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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3 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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4 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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5 "execution_count": 7, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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6 "id": "9aa0a6f7", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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7 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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8 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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9 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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10 "# ASIST module2 | map AST result to the CLSI breakporints with combination antibiotics\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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11 "# By rakesh4osdd@gmail.com, 06-Jun-2021\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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12 "import pandas as pd\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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13 "import re\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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14 "import sys" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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15 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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16 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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17 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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18 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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19 "execution_count": 8, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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20 "id": "9af8387e", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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21 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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22 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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23 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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24 "#print(pd.__version__, re.__version__)" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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25 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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26 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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27 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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28 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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29 "execution_count": 9, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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30 "id": "73d0783c", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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31 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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32 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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33 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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34 "# compare two MIC value strings\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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35 "def check_mic(mic1,mic2,mic_type):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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36 " #print(mic1,mic2,mic_type)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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37 " try:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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38 " if '/' in mic1:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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39 " m1a = mic1.split('/')[0]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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40 " m1b = mic1.split('/')[1]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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41 " if float(m1a)==0 or float(m1b)==0:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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42 " strain_type='Strain could not be classified'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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43 " return(strain_type) \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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44 " elif '/' in mic2:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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45 " m1a = mic1\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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46 " if float(m1a)==0:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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47 " strain_type='Strain could not be classified'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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48 " return(strain_type) \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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49 " m1b = '1'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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50 " elif float(mic1)==0:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
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51 " strain_type='Strain could not be classified'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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52 " return(strain_type)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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53 " else:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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54 " m1a = mic1\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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55 " \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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56 " if '-' in mic2:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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57 " m2a = mic2.split('-')[0]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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58 " m2b = mic2.split('-')[1] \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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59 " \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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60 " except ValueError:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
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61 " strain_type='Strain could not be classified' \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
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62 " return(strain_type)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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63 " try:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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64 " if '-' in mic2 and mic_type == 'i': # for intermediate only\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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65 " if '/' in mic2:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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66 " m2a = mic2.split('-')[0].split('/')[0]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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67 " m2b = mic2.split('-')[0].split('/')[1]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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68 " m2aa = mic2.split('-')[1].split('/')[0]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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69 " m2bb = mic2.split('-')[1].split('/')[1]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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70 " if (float(m2aa)>=float(m1a)>=float(m2a) and float(m2bb)>=float(m1b)>=float(m2b)):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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71 " #print('intermediate')\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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72 " m_type='Intermediate'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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73 " else:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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74 " #print('not define')\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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75 " m_type='Strain could not be classified'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
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76 " else:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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77 " m2a = mic2.split('-')[0]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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78 " m2b = mic2.split('-')[1] \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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79 " if (float(m2b)>=float(m1a)>=float(m2a)):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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80 " #print('intermediate')\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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81 " m_type='Intermediate'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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82 " else:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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83 " #print('not define')\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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84 " m_type='Strain could not be classified' \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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85 " #print (m1a,m1b,m2a,m2b,m2aa,m2bb)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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86 " elif '/' in mic2:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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87 " m2a = mic2.split('/')[0]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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88 " m2b = mic2.split('/')[1]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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89 " #print(m1a,m1b,m2a,m2b,mic_type)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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90 " if (mic_type=='s' and (float(m1a)<=float(m2a) and float(m1b)<=float(m2b))):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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91 " m_type='Susceptible'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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92 " elif (mic_type=='r' and (float(m1a)>=float(m2a) and float(m1b)>=float(m2b))):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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93 " m_type='Resistant'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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94 " elif (mic_type=='i' and (float(m1a)==float(m2a) and float(m1b)==float(m2b))):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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95 " m_type='Intermediate'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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96 " else:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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97 " m_type='Strain could not be classified'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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98 " elif '-' in mic2:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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99 " m_type='Strain could not be classified'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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100 " else:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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101 " m2a=mic2\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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102 " if (mic_type=='s' and (float(m1a)<=float(m2a))):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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103 " m_type='Susceptible'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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104 " elif (mic_type=='r' and (float(m1a)>=float(m2a))):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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105 " m_type='Resistant'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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106 " elif (mic_type=='i' and (float(m1a)==float(m2a))):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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107 " m_type='Intermediate'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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108 " else:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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109 " m_type='Strain could not be classified' \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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110 " except IndexError:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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111 " strain_type='Strain could not be classified' \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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112 " return(strain_type)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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113 " \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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114 " return(m_type)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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115 "\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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116 "#check_mic('65','32-64','i')" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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117 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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118 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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119 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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120 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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121 "execution_count": 10, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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122 "id": "4d2ab1b1", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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123 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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124 "outputs": [], |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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125 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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126 "# compare MIC value in pandas list\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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127 "def sus_res_int(mic):\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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128 " #print(mic)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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129 " o_mic = mic[0].replace(' ', '')\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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130 " s_mic = mic[1].replace(' ', '')\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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131 " r_mic = mic[2].replace(' ', '')\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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132 " i_mic = mic[3].replace(' ', '')\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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133 " try:\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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134 " if check_mic(o_mic,s_mic,'s')=='Susceptible':\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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135 " strain_type='Susceptible'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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136 " elif check_mic(o_mic,r_mic,'r')=='Resistant':\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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137 " strain_type='Resistant'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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138 " elif check_mic(o_mic,i_mic,'i')=='Intermediate':\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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139 " strain_type='Intermediate' \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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140 " else:\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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141 " strain_type='Strain could not be classified'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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142 " except ValueError:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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143 " strain_type='Strain could not be classified' \n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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144 " return(strain_type)\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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145 "\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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146 "#mic=['128','16/4','128/4','32/4-64/4']\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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147 "#sus_res_int(mic)" |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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148 ] |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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149 }, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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150 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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151 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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152 "execution_count": 11, |
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153 "id": "0e22ef0d", |
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154 "metadata": {}, |
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155 "outputs": [ |
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156 { |
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157 "ename": "IndexError", |
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158 "evalue": "list index out of range", |
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159 "output_type": "error", |
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160 "traceback": [ |
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161 "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", |
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162 "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)", |
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163 "\u001b[0;32m<ipython-input-11-26f141926f14>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0minput_user\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0margv\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0minput_clsi\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0margv\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0moutput_table\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0margv\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m3\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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164 "\u001b[0;31mIndexError\u001b[0m: list index out of range" |
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165 ] |
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166 } |
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167 ], |
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168 "source": [ |
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169 "# for input argument\n", |
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170 "input_user = sys.argv[1]\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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171 "input_clsi = sys.argv[2]\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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172 "output_table = sys.argv[3]" |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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173 ] |
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174 }, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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175 { |
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176 "cell_type": "code", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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177 "execution_count": 49, |
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178 "id": "21d5fe63", |
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179 "metadata": {}, |
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180 "outputs": [], |
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181 "source": [ |
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182 "\"\"\"input_user='~/Jupyterlab_notebook/ASIST_module/strain_profiles_16k.csv.csv'\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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183 "#input_user='test-data/input2.csv'\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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184 "input_clsi='test-data/clsi.csv'\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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185 "output_profile='test-data/input2_profile.csv'\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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186 "#output_table='test-data/input2_table.csv'\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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187 "output_table='/home/rakesh/Jupyterlab_notebook/ASIST_module/strain_profiles_16k_table.csv'\"\"\"" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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188 ] |
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189 }, |
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190 { |
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191 "cell_type": "code", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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192 "execution_count": 60, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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193 "id": "1e64b025", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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194 "metadata": {}, |
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195 "outputs": [], |
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196 "source": [ |
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197 "# read user AST data with selected 3 columns\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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198 "strain_mic=pd.read_csv(input_user, sep=',', usecols =['Strain name', 'Antibiotics', 'MIC'],na_filter=False)\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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199 "#strain_mic" |
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200 ] |
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201 }, |
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202 { |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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203 "cell_type": "code", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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204 "execution_count": 61, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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205 "id": "0d30ddc3", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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206 "metadata": {}, |
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207 "outputs": [], |
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208 "source": [ |
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209 "clsi_bp=pd.read_csv(input_clsi,sep=',')\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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210 "\n", |
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211 "#clsi_bp[clsi_bp[['Antibiotics', 'Susceptible']].duplicated()].shape" |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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212 ] |
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213 }, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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214 { |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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215 "cell_type": "code", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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216 "execution_count": 62, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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217 "id": "a818676d", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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218 "metadata": {}, |
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219 "outputs": [], |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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220 "source": [ |
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221 "#clsi_bp\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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222 "#strain_mic" |
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223 ] |
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224 }, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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225 { |
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226 "cell_type": "code", |
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227 "execution_count": 64, |
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228 "id": "c2aae757", |
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229 "metadata": {}, |
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230 "outputs": [], |
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231 "source": [ |
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232 "# warn user for duplicate files\n", |
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233 "input_dups=strain_mic[strain_mic[['Strain name','Antibiotics']].duplicated()]\n", |
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234 "if (input_dups.shape[0] == 0):\n", |
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235 " #print( \"No duplicates\")\n", |
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236 " pass\n", |
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237 "else:\n", |
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238 " with open(output_table, \"w\") as file_object:\n", |
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239 " # Append 'hello' at the end of file\n", |
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240 " 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')\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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241 " input_dups.to_csv(output_table,na_rep='NA', mode='a')\n", |
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242 " exit()" |
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243 ] |
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244 }, |
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245 { |
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246 "cell_type": "code", |
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247 "execution_count": 17, |
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248 "id": "c6b4c59b", |
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249 "metadata": {}, |
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250 "outputs": [], |
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251 "source": [ |
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252 "# convert MIC to numbers sMIC, rMIC\n", |
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253 "clsi_bp['s_mic'] =clsi_bp[['Susceptible']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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254 "clsi_bp['r_mic'] =clsi_bp[['Resistant']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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255 "clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))" |
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256 ] |
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257 }, |
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258 { |
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259 "cell_type": "code", |
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260 "execution_count": 18, |
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261 "id": "d0171f94", |
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262 "metadata": {}, |
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263 "outputs": [], |
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264 "source": [ |
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265 "#clsi_bp['i_mic'] = clsi_bp[['Intermediate']].applymap(lambda x: (re.sub(r'[^0-9.\\/-]', '', x)))" |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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266 ] |
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267 }, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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268 { |
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269 "cell_type": "code", |
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270 "execution_count": 19, |
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271 "id": "fe45b2dd", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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272 "metadata": {}, |
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273 "outputs": [], |
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274 "source": [ |
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275 "# Read only numbers in MIC values\n", |
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276 "#try:\n", |
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277 "strain_mic['o_mic']=strain_mic[['MIC']].applymap(lambda x: (re.sub(r'[^0-9.\\/]','', x)))\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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278 "#except TypeError:\n", |
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279 "# print('Waring: Error in MIC value')" |
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280 ] |
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281 }, |
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282 { |
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283 "cell_type": "code", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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284 "execution_count": 20, |
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285 "id": "ddbbe4d9", |
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286 "metadata": {}, |
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287 "outputs": [], |
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288 "source": [ |
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289 "#strain_mic" |
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290 ] |
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291 }, |
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292 { |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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293 "cell_type": "code", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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294 "execution_count": 21, |
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295 "id": "640508f1", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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296 "metadata": {}, |
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297 "outputs": [], |
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298 "source": [ |
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299 "# capitalize each Antibiotic Name for comparision with removing whitespace\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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300 "strain_mic['Strain name']=strain_mic['Strain name'].str.capitalize().str.replace(\" \",\"\")\n", |
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301 "strain_mic['Antibiotics']=strain_mic['Antibiotics'].str.capitalize().str.replace(\" \",\"\")\n", |
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302 "\n", |
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303 "clsi_bp['Antibiotics']=clsi_bp['Antibiotics'].str.capitalize().str.replace(\" \",\"\")" |
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304 ] |
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305 }, |
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306 { |
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307 "cell_type": "code", |
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308 "execution_count": 22, |
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309 "id": "b87426f4", |
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310 "metadata": {}, |
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311 "outputs": [], |
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312 "source": [ |
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313 "#find duplicate values in input files\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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314 "dups=strain_mic[strain_mic[['Strain name', 'Antibiotics']].duplicated(keep=False)]\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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315 "if dups.shape[0] != 0:\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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316 " print ('Please provide a single MIC value in input file for given duplicates combination of \\'Strain name and Antibiotics\\' to use the tool:-\\n',dups)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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317 " #exit()\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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318 "else:\n", |
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319 " #compare CLSI Antibiotics only\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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320 " #result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner', indicator=True)[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','_merge']]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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321 " try:\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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322 " result=pd.merge(strain_mic, clsi_bp, on='Antibiotics',how='inner')[['Strain name','Antibiotics', 'MIC', 'o_mic', 's_mic', 'r_mic','i_mic']]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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323 " except KeyError:\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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324 " print('Waring: Error in input Values')" |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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325 ] |
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326 }, |
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327 { |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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328 "cell_type": "code", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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329 "execution_count": 23, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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330 "id": "91bfc94d", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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331 "metadata": {}, |
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332 "outputs": [ |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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333 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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334 "data": { |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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335 "text/html": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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336 "<div>\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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337 "<style scoped>\n", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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338 " .dataframe tbody tr th:only-of-type {\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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339 " vertical-align: middle;\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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340 " }\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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341 "\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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342 " .dataframe tbody tr th {\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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343 " vertical-align: top;\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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344 " }\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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345 "\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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346 " .dataframe thead th {\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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347 " text-align: right;\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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348 " }\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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349 "</style>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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350 "<table border=\"1\" class=\"dataframe\">\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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351 " <thead>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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352 " <tr style=\"text-align: right;\">\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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353 " <th></th>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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354 " <th>Strain name</th>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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355 " <th>Antibiotics</th>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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356 " <th>MIC</th>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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357 " <th>o_mic</th>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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358 " </tr>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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359 " </thead>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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360 " <tbody>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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361 " </tbody>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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362 "</table>\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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363 "</div>" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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364 ], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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365 "text/plain": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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366 "Empty DataFrame\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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367 "Columns: [Strain name, Antibiotics, MIC, o_mic]\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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368 "Index: []" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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369 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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370 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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371 "execution_count": 23, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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372 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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373 "output_type": "execute_result" |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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374 } |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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375 ], |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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376 "source": [ |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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377 "dups.head()" |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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378 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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379 }, |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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380 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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381 "cell_type": "code", |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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382 "execution_count": 132, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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383 "id": "b171f205", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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384 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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385 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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386 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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387 "#compare MIC values and assign Susceptible and Resistant to Strain\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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388 "#try:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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389 "result[['CLSI_profile']] = result[['o_mic','s_mic','r_mic','i_mic']].apply(sus_res_int,axis = 1)\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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390 "#except ValueError:\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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391 "# print('Waring: Error in input MIC value')" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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392 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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393 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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394 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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395 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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396 "execution_count": 133, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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397 "id": "3336fd92", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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398 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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399 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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400 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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401 "#result" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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402 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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403 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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404 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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405 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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406 "execution_count": 134, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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407 "id": "f0dacfd1", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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408 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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409 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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410 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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411 "#result[['Strain name', 'Antibiotics', 'MIC','s_mic','r_mic','CLSI_profile']].to_csv(output_profile,sep=',', index=False, encoding='utf-8-sig')" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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412 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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413 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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414 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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415 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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416 "execution_count": 135, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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417 "id": "3d8d03f7", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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418 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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419 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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420 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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421 "#create a pivot table for ASIST\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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422 "table=result[['Strain name', 'Antibiotics','CLSI_profile']].drop_duplicates()\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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423 "result_table=pd.pivot_table(table, values ='CLSI_profile', index =['Strain name'],columns =['Antibiotics'], aggfunc = lambda x: ' '.join(x))" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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424 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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425 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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426 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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427 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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428 "execution_count": 136, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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429 "id": "7d7223a3", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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430 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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431 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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432 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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433 "#result_table" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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434 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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435 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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436 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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437 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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438 "execution_count": 137, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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439 "id": "8a41b2ef", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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440 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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441 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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442 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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443 "#result_table.to_csv(output_table,na_rep='NA')" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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444 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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445 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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446 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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447 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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448 "execution_count": 138, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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449 "id": "8c9e5f87", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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450 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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451 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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452 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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453 "# reorder the Antibiotics for ASIST\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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454 "clsi_ab=['Amikacin','Tobramycin','Gentamycin','Netilmicin','Imipenem','Meropenem','Doripenem','Ciprofloxacin','Levofloxacin',\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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455 " 'Piperacillin/tazobactam','Ticarcillin/clavulanicacid','Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime',\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
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456 " 'Trimethoprim/sulfamethoxazole','Ampicillin/sulbactam','Colistin','Polymyxinb','Tetracycline','Doxicycline ',\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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457 " 'Minocycline']\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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458 "result_selected=result_table.filter(clsi_ab)" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
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459 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
460 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
461 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
462 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
463 "execution_count": 139, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
464 "id": "cdf43afb", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
465 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
466 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
467 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
468 "#print(result_selected.shape, result_table.shape)" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
469 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
470 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
471 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
472 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
473 "execution_count": 140, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
474 "id": "c4c4df30", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
475 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
476 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
477 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
478 "#result_selected.insert(0,'Resistance_phenotype','')" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
479 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
480 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
481 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
482 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
483 "execution_count": 141, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
484 "id": "9adb2703", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
485 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
486 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
487 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
488 "#rename headers\n", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
489 "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'} )" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
490 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
491 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
492 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
493 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
494 "execution_count": 142, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
495 "id": "50e6cf5f", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
496 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
497 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
498 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
499 "#result_selected" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
500 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
501 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
502 { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
503 "cell_type": "code", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
504 "execution_count": 144, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
505 "id": "2833671c", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
506 "metadata": {}, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
507 "outputs": [], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
508 "source": [ |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
509 "result_selected.to_csv(output_table,na_rep='NA')" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
510 ] |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
511 } |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
512 ], |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
513 "metadata": { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
514 "kernelspec": { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
515 "display_name": "Python 3", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
516 "language": "python", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
517 "name": "python3" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
518 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
519 "language_info": { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
520 "codemirror_mode": { |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
521 "name": "ipython", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
522 "version": 3 |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
523 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
524 "file_extension": ".py", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
525 "mimetype": "text/x-python", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
526 "name": "python", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
527 "nbconvert_exporter": "python", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
528 "pygments_lexer": "ipython3", |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
529 "version": "3.7.10" |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
530 } |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
531 }, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
532 "nbformat": 4, |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
533 "nbformat_minor": 5 |
7dcc0e93288b
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents:
diff
changeset
|
534 } |