Update app.py

app.py

@@ -6,6 +6,7 @@ import SigProfilerMatrixGenerator
 from SigProfilerMatrixGenerator import install as genInstall
 import shutil
 import os
+import re
 from SigProfilerExtractor import sigpro as sig
 import sys
 import numpy as np
@@ -29,7 +30,7 @@ def show_pdf(file_path):
     st.markdown(pdf_display, unsafe_allow_html=True)
 
 #@st.cache_data(experimental_allow_widgets=True)
-def showdl(file_to_lookat,to_dl_sbs,to_dl_indel,to_dl_dbs,to_dl_sbs_text,to_dl_indel_text,to_dl_dbs_text):
+def showdl(file_to_lookat,to_dl_sbs,to_dl_indel,to_dl_dbs,to_dl_sbs_text,to_dl_indel_text,to_dl_dbs_text,to_dl_sbs_summary_text,to_dl_id_summary_text,to_dl_dbs_summary_text):
     for j in np.arange(0,len(to_dl_sbs)):
         if to_dl_sbs[j] != []:
             download_link1 = f'<a href="data:application/octet-stream;base64, \
@@ -38,10 +39,14 @@ def showdl(file_to_lookat,to_dl_sbs,to_dl_indel,to_dl_dbs,to_dl_sbs_text,to_dl_i
                       
             download_link2 = f'<a href="data:application/octet-stream;base64, \
                 {base64.b64encode(to_dl_sbs_text[j]).decode()}" download=" \
-                {file_to_lookat[j].name}SBS.txt">Download {file_to_lookat[j].name} Single Base Substition table</a>'  
+                {file_to_lookat[j].name}SBS.txt">Download {file_to_lookat[j].name} Single Base Substition table</a>' 
+            download_link3 = f'<a href="data:application/octet-stream;base64, \
+                {base64.b64encode(to_dl_sbs_summary_text[j]).decode()}" download=" \
+                {file_to_lookat[j].name}SBS_summary.txt">Download {file_to_lookat[j].name} Single Base Substition table</a>'            
             st.markdown(download_link1, unsafe_allow_html=True)  
 
-            st.markdown(download_link2, unsafe_allow_html=True)        
+            st.markdown(download_link2, unsafe_allow_html=True)  
+            st.markdown(download_link3, unsafe_allow_html=True)  
 
     for j in np.arange(0,len(to_dl_indel)): 
         if to_dl_indel[j] != []:
@@ -90,6 +95,11 @@ def dl(valforkey):
         PDFbyte1 = pdf_file.read()    
     with open("output/SBS96/Samples.txt","rb") as txt_file:
         Txtbyte1 = txt_file.read()   
+        txt_file.close()    
+    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']]    
         #st.download_button(label="Download image with single base substitution profiles", key=valforkey,
         #                    data=PDFbyte1,
         #                    file_name="SBS.pdf",
@@ -100,17 +110,27 @@ def dl(valforkey):
             PDFbyte2 = pdf_file.read()
         with open("output/ID83/Samples.txt","rb") as txt_file:
             Txtbyte2 = txt_file.read()
+        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']]            
     else:
         PDFbyte2 = []
-        Txtbyte2 = []        
+        Txtbyte2 = []  
+        summary_table_id_all=[]
     if glob.glob("output/DBS78/Suggested_Solution/COSMIC_DBS78_Decomposed_Solution/DBS78_Decomposition_Plots.pdf") != []:
         with open("output/DBS78/Suggested_Solution/COSMIC_DBS78_Decomposed_Solution/DBS78_Decomposition_Plots.pdf", "rb") as pdf_file:
             PDFbyte3 = pdf_file.read()
         with open("output/DBS78/Samples.txt","rb") as txt_file:
             Txtbyte3 = txt_file.read() 
+        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']]     
     else:
         PDFbyte3 = []
         Txtbyte3=[]
+        summary_table_dbs_all=[]
     os.system('rm -r output')  
     os.system('rm -r input')       
     #os.remove("output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf")
@@ -126,7 +146,7 @@ def dl(valforkey):
         #                    data=PDFbyte2,
         #                    file_name="idel.pdf",
         #                    mime='application/octet-stream')
-    return PDFbyte1,PDFbyte2,PDFbyte3,Txtbyte1,Txtbyte2,Txtbyte3  
+    return PDFbyte1,PDFbyte2,PDFbyte3,Txtbyte1,Txtbyte2,Txtbyte3, summary_table_sbs_all, summary_table_id_all,summary_table_dbs_all
 
 
 
@@ -172,7 +192,11 @@ if file_to_lookat !=[] and sub:
     to_dl_dbs=[]
     to_dl_sbs_text=[]
     to_dl_indel_text=[]
-    to_dl_dbs_text=[]    
+    to_dl_dbs_text=[]  
+    to_dl_sbs_summary_text=[]
+    to_dl_id_summary_text=[]
+    to_dl_dbs_summary_text=[]
+    
     for j in np.arange(0,len(file_to_lookat)):
         if not os.path.exists('input'):
             os.mkdir('input')
@@ -196,7 +220,7 @@ if file_to_lookat !=[] and sub:
             
     
         if file_to_lookat !=[] and glob.glob('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/*pdf'):               
-            sbs_result,indel_result,dbs_result,sbs_text,indel_text,dbs_text=dl(j)
+            sbs_result,indel_result,dbs_result,sbs_text,indel_text,dbs_text,summary_sbs,dummary_id,summary_dbs=dl(j)
             
             to_dl_sbs.append(sbs_result)
             to_dl_sbs_text.append(sbs_text)
@@ -204,6 +228,9 @@ if file_to_lookat !=[] and sub:
             to_dl_indel_text.append(indel_text)
             to_dl_dbs.append(dbs_result)
             to_dl_dbs_text.append(dbs_text)
+            to_dl_sbs_summary_text.append(summary_sbs)
+            to_dl_id_summary_text.append(summary_id)
+            to_dl_dbs_summary_text.append(summary_dbs)
       
         #show_pdf('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf')
 
@@ -211,7 +238,7 @@ if file_to_lookat !=[] and sub:
 
             remove_old_vcf() 
            
-    showdl(file_to_lookat,to_dl_sbs,to_dl_indel,to_dl_dbs,to_dl_sbs_text,to_dl_indel_text,to_dl_dbs_text)         
+    showdl(file_to_lookat,to_dl_sbs,to_dl_indel,to_dl_dbs,to_dl_sbs_text,to_dl_indel_text,to_dl_dbs_text,to_dl_sbs_summary_text,to_dl_id_summary_text,to_dl_dbs_summary_text)         
     components.iframe("https://cancer.sanger.ac.uk/signatures/sbs/", height=3000,width=800)
     #show_pdf('output/ID83/Suggested_Solution/COSMIC_ID83_Decomposed_Solution/ID83_Decomposition_Plots.pdf')
     #components.iframe("https://cancer.sanger.ac.uk/signatures/id/",height=1000,width=800)