Update app.py

app.py

@@ -8,6 +8,7 @@ import shutil
 import os
 import re
 from SigProfilerExtractor import sigpro as sig
+from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as datadump  
 import sys
 import numpy as np
 import pandas as pd
@@ -34,6 +35,16 @@ def show_pdf(file_path):
     pdf_display = f'<iframe src="data:application/pdf;base64,{base64_pdf}" width="1500" height="1000" type="application/pdf"></iframe>'
     st.markdown(pdf_display, unsafe_allow_html=True)
 
+def showdl_counts(file_to_lookat,to_dl_sbs96,to_dl_sbs1536):
+    download_link1 = f'<a href="data:application/octet-stream;base64, \
+            {base64.b64encode(to_dl_sbs96[j]).decode()}" download=" \
+            {file_to_lookat[j].name}96SBS.txt">Download {file_to_lookat[j].name} Single Base Substition (96) table</a>' 
+    
+    download_link2 = f'<a href="data:application/octet-stream;base64, \
+            {base64.b64encode(to_dl_sbs1536[j]).decode()}" download=" \
+            {file_to_lookat[j].name}1536SBS.txt">Download {file_to_lookat[j].name} Single Base Substition (1536) table</a>' 
+    st.markdown(download_link1, unsafe_allow_html=True) 
+    st.markdown(download_link2, 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,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)):
@@ -98,7 +109,16 @@ def showdl(file_to_lookat,to_dl_sbs,to_dl_indel,to_dl_dbs,to_dl_sbs_text,to_dl_i
         #                    mime='application/octet-stream')
 
 
+def dl_counts(valforkey):
+    with open("SBS96.txt","rb") as txt_file:
+        sbs96_all_bytes = txt_file.read()
+        txt_file.close()    
+    with open("SBS1536","rb") as txt_file:
+        sbs96_all_bytes = txt_file.read() 
+        txt_file.close()
+    return sbs96_all_bytes, sbs1536_all_bytes
 
+    
 def dl(valforkey):
     #breakpoint()
     seev=glob.glob('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/*pdf')
@@ -223,6 +243,8 @@ if file_to_lookat !=[] and sub:
     to_dl_sbs_summary_text=[]
     to_dl_id_summary_text=[]
     to_dl_dbs_summary_text=[]
+    to_dl_sbs96=[]
+    to_dl_sbs1536=[]
     
     for j in np.arange(0,len(file_to_lookat)):
         if not os.path.exists('input'):
@@ -267,31 +289,48 @@ if file_to_lookat !=[] and sub:
         #vcfuse=glob.glob('file_to_lookat[0].name')[0]
         #shutil.copy2(vcfuse,'input/'+vcfuse)
         #pdb.set_trace()
+        if no_profiles_only_counts == True:
+            refgen="GRCh37"
+            project = "input"
+            project_name = project.split("/")[-1]
+            with st.spinner('computing counts only'):    
+                data = datadump.SigProfilerMatrixGeneratorFunc(project_name, refgen, project, exome=False,  bed_file=None, chrom_based=False, plot=False, gs=False)
+                data['96'].to_csv('sbs96.txt',sep='\t',header=False,index=True)
+                data['1536'].to_csv('sbs1536.txt',sep='\t',header=False,index=True)
+                sbs96_result,sbs1536_result=dl_counts(j)
+                to_dl_sbs96.append(sbs96_result)
+                to_dl_sbs1536.append(sbs1536_result)
+                remove_old_vcf()
+
+        else:    
             
             with st.spinner('computing signatures'):
                 sig.sigProfilerExtractor("vcf", "output", "input", minimum_signatures=1, maximum_signatures=3,nmf_test_conv= 1000,nmf_tolerance= 1e-10,max_nmf_iterations=100000,min_nmf_iterations= 1000)
-            
+                
+        
+            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,summary_sbs,summary_id,summary_dbs=dl(j)
+                
+                to_dl_sbs.append(sbs_result)
+                to_dl_sbs_text.append(sbs_text)
+                to_dl_indel.append(indel_result)
+                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')
     
-        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,summary_sbs,summary_id,summary_dbs=dl(j)
-            
-            to_dl_sbs.append(sbs_result)
-            to_dl_sbs_text.append(sbs_text)
-            to_dl_indel.append(indel_result)
-            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')
-
-
-
-            remove_old_vcf() 
+    
+    
+                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,to_dl_sbs_summary_text,to_dl_id_summary_text,to_dl_dbs_summary_text)         
+    if no_profiles_only_counts == True:
+        showdl_counts(file_to_lookat,to_dl_sbs96,to_dl_sbs1536)
+    else:
+        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)