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annotate asist_dynamic.py @ 0:c1a77856070c draft

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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
author rakesh4osdd
date Sat, 26 Jun 2021 07:27:53 +0000
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children 734777d3c253
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c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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1 #!/usr/bin/env python
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2 # coding: utf-8
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4 # In[1309]:
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7 #ASIST program for phenotype based on Antibiotics profile
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8 # create a profile based on selected antibiotics only
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9 # rakesh4osdd@gmail.com, 14-June-2021
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12 # In[1403]:
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c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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15 import pandas as pd
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16 import sys
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17 import os
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18 from collections import Counter
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21 # In[ ]:
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24 input_file=sys.argv[1]
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25 output_file=sys.argv[2]
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28 # In[1362]:
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31 # strain_profile to phenotype condition
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32 def s_phen(sus,res,na,pb_sus):
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33 if (sus>0 and res==0 and na>=0):
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34 #print('Possible Susceptible')
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35 phen='Possible Susceptible'
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36 elif (sus>=0 and 3<=res<7 and na>=0 and pb_sus==0):
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37 #print('Possible MDR')
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38 phen='Possible MDR'
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39 elif (sus>=0 and 7<=res<9 and na>=0 and pb_sus==0):
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40 #print('Possible XDR')
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41 phen='Possible XDR'
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42 #special cases
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43 elif (sus>=1 and res>0 and na>=0 and pb_sus==1):
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44 #print('Possible XDR')
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45 phen='Possible XDR'
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46 #special cases
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47 elif (sus>0 and res==9 and na>=0):
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48 #print('Possible XDR')
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49 phen='Possible XDR'
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50 elif (sus==0 and res==9 and na>=0):
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51 #print('Possible TDR')
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52 phen='Possible TDR'
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53 else:
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54 #print('Strain could not be classified')
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55 phen='Strain could not be classified'
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56 return(phen)
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58 #print(s_phen(1,9,0,0))
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61 # In[1363]:
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64 # define Antibiotic groups as per antibiotic of CLSI breakpoints MIC
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65 #Aminoglycoside
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66 cat1=['Amikacin','Tobramycin','Gentamycin','Netilmicin']
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67 #Beta-lactams- Carbapenems
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68 cat2=['Imipenem','Meropenam','Doripenem']
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69 #Fluoroquinolone
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70 cat3=['Ciprofloxacin','Levofloxacin']
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71 #Beta-lactam inhibitor
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72 cat4=['Piperacillin/tazobactam','Ticarcillin/clavulanicacid']
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73 #Cephalosporin
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74 cat5=['Cefotaxime','Ceftriaxone','Ceftazidime','Cefepime']
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75 #Sulfonamides
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76 cat6=['Trimethoprim/sulfamethoxazole']
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77 #Penicillins/beta-lactamase
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78 cat7=['Ampicillin/sulbactam']
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79 #Polymyxins
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80 cat8=['Colistin','Polymyxinb']
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81 #Tetracycline
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82 cat9=['Tetracycline','Doxicycline','Minocycline']
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83
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84 def s_profiler(pd_series):
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85 #print(type(pd_series),'\n', pd_series)
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86 #create a dictionary of dataframe series
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87 cats={'s1':cat1,'s2':cat2,'s3':cat3,'s4':cat4,'s5':cat5,'s6':cat6,'s7':cat7,'s8':cat8,'s9':cat9}
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88 # find the antibiotics name in input series
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
rakesh4osdd
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89 for cat in cats:
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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90 #print(cats[cat])
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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91 cats[cat]=pd_series.filter(cats[cat])
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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92 #print(cats[cat])
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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93 #define res,sus,na,pb_sus
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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94 res=0
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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95 sus=0
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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96 na=0
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97 pb_sus=0
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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98 # special case of 'Polymyxin b' for its value
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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99 if 'Polymyxinb' in pd_series:
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100 ctp=cats['s8']['Polymyxinb'].strip().lower()
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
rakesh4osdd
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101 if ctp == 'susceptible':
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102 pb_sus=1
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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103 #print((ctp,p_sus))
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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104 # check all categories
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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105 for cat in cats:
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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106 #ctp=cats['s8'].iloc[i:i+1].stack().value_counts().to_dict()
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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107 #print(ctp)
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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108 # Pandas series
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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109 ct=cats[cat].value_counts().to_dict()
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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110 #print(ct)
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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111 # remove whitespace and convert to lowercase words
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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112 ct = {k.strip().lower(): v for k, v in ct.items()}
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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113 #print(ct)
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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114 k=Counter(ct)
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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115 #j=Counter(ct)+Counter(j)
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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116 #print(j)
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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117 # category wise marking
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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118 if k['resistant']>=1:
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119 res=res+1
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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120 if k['susceptible']>=1:
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121 sus=sus+1
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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122 if k['na']>=1:
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123 na=na+1
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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124 #print(s_phen(sus,res,na,pb_sus))
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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125 return(s_phen(sus,res,na,pb_sus))
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126
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127
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128 # In[1397]:
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129
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130
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131 #input_file='input2.csv_table.csv'
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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132 #output_file=input_file+'_output.txt'
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133 strain_profile=pd.read_csv(input_file, sep=',',na_filter=False,skipinitialspace = True)
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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134
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135
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136 # In[1387]:
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137
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138
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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139 old_strain_name=strain_profile.columns[0]
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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140 new_strain_name=old_strain_name.capitalize().strip().replace(' ', '')
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141
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142
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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143 # In[1388]:
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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144
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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145
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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146 # make header capitalization, remove leading,lagging, and multiple whitespace for comparision
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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147 strain_profile.columns=strain_profile.columns.str.capitalize().str.strip().str.replace('\s+', '', regex=True)
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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148 #print(strain_profile.columns)
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149 #strain_profile.head()
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150 #strain_profile.columns
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151
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152
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153 # In[1389]:
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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154
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155
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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156 # add new column in dataframe on second position
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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157 strain_profile.insert(1, 'Strain phenotype','')
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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158 #strain_profile.head()
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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159
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160
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161 # In[1390]:
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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162
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163
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164 strain_profile['Strain phenotype'] = strain_profile.apply(lambda x: (s_profiler(x)), axis=1)
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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165
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166
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167 # In[1391]:
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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168
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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169
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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170 #strain_profile.head()
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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171
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172
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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173 # In[1392]:
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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174
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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175
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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176 #rename headers for old name
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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177 strain_profile=strain_profile.rename(columns = {new_strain_name:old_strain_name, 'Ticarcillin/clavulanicacid':'Ticarcillin/ clavulanic acid','Piperacillin/tazobactam':'Piperacillin/ tazobactam','Trimethoprim/sulfamethoxazole': 'Trimethoprim/ sulfamethoxazole','Ampicillin/sulbactam':'Ampicillin/ sulbactam', 'Polymyxinb': 'Polymyxin B'} )
c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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180 # In[1404]:
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181
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c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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183 #strain_profile
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c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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186 # In[1394]:
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c1a77856070c "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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189 strain_profile.to_csv(output_file,na_rep='NA',index=False)
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190