Mercurial > repos > rakesh4osdd > asist
diff asist_dynamic.py @ 3:734777d3c253 draft
Deleted selected files test
author | rakesh4osdd |
---|---|
date | Wed, 30 Jun 2021 05:35:56 +0000 |
parents | c1a77856070c |
children |
line wrap: on
line diff
--- a/asist_dynamic.py Mon Jun 28 15:05:17 2021 +0000 +++ b/asist_dynamic.py Wed Jun 30 05:35:56 2021 +0000 @@ -9,7 +9,7 @@ # rakesh4osdd@gmail.com, 14-June-2021 -# In[1403]: +# In[1]: import pandas as pd @@ -18,18 +18,20 @@ from collections import Counter -# In[ ]: +# In[176]: input_file=sys.argv[1] output_file=sys.argv[2] +#input_file='test-data/asist_input.csv' +#output_file='test-data/asist_output.csv' -# In[1362]: +# In[177]: # strain_profile to phenotype condition -def s_phen(sus,res,na,pb_sus): +def s_phen(sus,res,intm,na,pb_sus): if (sus>0 and res==0 and na>=0): #print('Possible Susceptible') phen='Possible Susceptible' @@ -52,13 +54,13 @@ phen='Possible TDR' else: #print('Strain could not be classified') - phen='Strain could not be classified' + phen='Strain could not be classified ('+ str(intm)+' | ' + str(na) +')' return(phen) #print(s_phen(1,9,0,0)) -# In[1363]: +# In[178]: # define Antibiotic groups as per antibiotic of CLSI breakpoints MIC @@ -90,9 +92,10 @@ #print(cats[cat]) cats[cat]=pd_series.filter(cats[cat]) #print(cats[cat]) - #define res,sus,na,pb_sus + #define res,sus,intm,na,pb_sus res=0 sus=0 + intm=0 na=0 pb_sus=0 # special case of 'Polymyxin b' for its value @@ -119,13 +122,16 @@ res=res+1 if k['susceptible']>=1: sus=sus+1 + if k['intermediate']>=1: + intm=intm+1 if k['na']>=1: na=na+1 - #print(s_phen(sus,res,na,pb_sus)) - return(s_phen(sus,res,na,pb_sus)) + #print(sus,res,intm,na,pb_sus) + #print(s_phen(sus,res,intm,na,pb_sus)) + return(s_phen(sus,res,intm,na,pb_sus)) -# In[1397]: +# In[179]: #input_file='input2.csv_table.csv' @@ -133,14 +139,14 @@ strain_profile=pd.read_csv(input_file, sep=',',na_filter=False,skipinitialspace = True) -# In[1387]: +# In[180]: old_strain_name=strain_profile.columns[0] new_strain_name=old_strain_name.capitalize().strip().replace(' ', '') -# In[1388]: +# In[181]: # make header capitalization, remove leading,lagging, and multiple whitespace for comparision @@ -150,7 +156,7 @@ #strain_profile.columns -# In[1389]: +# In[182]: # add new column in dataframe on second position @@ -158,33 +164,54 @@ #strain_profile.head() -# In[1390]: +# In[183]: strain_profile['Strain phenotype'] = strain_profile.apply(lambda x: (s_profiler(x)), axis=1) -# In[1391]: +# In[184]: #strain_profile.head() -# In[1392]: +# In[185]: #rename headers for old name 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'} ) -# In[1404]: +# In[186]: + + +#strain_profile.columns + + +# In[187]: #strain_profile -# In[1394]: +# In[188]: strain_profile.to_csv(output_file,na_rep='NA',index=False) + +# In[189]: + + +# Open a file with access mode 'a' +with open(output_file, "a") as file_object: + # Append 'hello' at the end of file + file_object.write("Note: \n1. 'MDR': Multidrug-resistant, 'XDR': Extensively drug-resistant, 'TDR':totally drug resistant, NA': Data Not Available.\n2. 'Strain could not be classified' numbers follow the format as ('Number of antibiotics categories count as Intermediate' | 'Number of antibiotics categories count as NA')") + + +# In[ ]: + + + +