Update app.py

app.py

@@ -104,8 +104,8 @@ def dl(valforkey):
     hh=pd.read_table('output/SBS96/Samples.txt') 
     hh['nums']=hh.iloc[:,1]
     hh['mutation_simple']=hh['MutationType'].apply(lambda x: re.sub('].$','',re.sub('^.\[','',x)))    
-    summary_table_sbs_all=hh.groupby('mutation_simple').apply(lambda x: x.sum())[['mutation_simple','nums']]   
-    summary_table_sbs_all.to_csv('sbs_summary.txt',sep='\t',header=False,index=False)
+    summary_table_sbs_all=hh.groupby('mutation_simple').apply(lambda x: x.sum())[['nums']]   
+    summary_table_sbs_all.to_csv('sbs_summary.txt',sep='\t',header=False,index=True)
     with open("sbs_summary.txt","rb") as txt_file:
         summary_table_sbs_all_bytes = txt_file.read()   
         txt_file.close()     
@@ -122,8 +122,8 @@ def dl(valforkey):
         hh2=pd.read_table('output/ID83/Samples.txt') 
         hh2['nums']=hh2.iloc[:,1]
         hh2['mutation_simple']=hh2['MutationType'].apply(lambda x: re.sub('].$','',re.sub('^.\[','',x)))    
-        summary_table_id_all=hh2.groupby('mutation_simple').apply(lambda x: x.sum())[['mutation_simple','nums']] 
-        summary_table_id_all.to_csv('id_summary.txt',sep='\t',header=False,index=False)
+        summary_table_id_all=hh2.groupby('mutation_simple').apply(lambda x: x.sum())[['nums']] 
+        summary_table_id_all.to_csv('id_summary.txt',sep='\t',header=False,index=True)
         with open("id_summary.txt","rb") as txt_file:
             summary_table_id_all_bytes = txt_file.read()   
             txt_file.close()        
@@ -139,8 +139,8 @@ def dl(valforkey):
         hh3=pd.read_table('output/DBS78/Samples.txt') 
         hh3['nums']=hh3.iloc[:,1]
         hh3['mutation_simple']=hh3['MutationType'].apply(lambda x: re.sub('].$','',re.sub('^.\[','',x)))    
-        summary_table_dbs_all=hh3.groupby('mutation_simple').apply(lambda x: x.sum())[['mutation_simple','nums']]  
-        summary_table_dbs_all.to_csv('dbs_summary.txt',sep='\t',header=False,index=False)
+        summary_table_dbs_all=hh3.groupby('mutation_simple').apply(lambda x: x.sum())[['nums']]  
+        summary_table_dbs_all.to_csv('dbs_summary.txt',sep='\t',header=False,index=True)
         with open("dbs_summary.txt","rb") as txt_file:
             summary_table_dbs_all_bytes = txt_file.read()   
             txt_file.close()           
@@ -246,14 +246,13 @@ if file_to_lookat !=[] and sub:
             tovcf.to_csv(nameuse,sep='\t',header=False, index=False)
             st.write('original file read as:')
             st.write(table_of_penn_file)
-            #st.write(tovcf)
+            st.write('file after liftover:')
+            st.write(tovcf)
             #st.write(nameuse)
             with open(nameuse,"rb") as txt_file:
                 bytes_data=txt_file.read()
             txt_file.close()
             with open(os.path.join("input",nameuse),"wb") as f:
-                st.write('file after liftover:')
-                st.write(os.path.join("input",nameuse))
                 f.write(bytes_data)
             f.close()
             seev=glob.glob('input/*')