Update app.py

app.py

@@ -8,6 +8,7 @@ import shutil
 import os
 from SigProfilerExtractor import sigpro as sig
 import sys
+import numpy as np
 import base64
 import streamlit.components.v1 as components
 
@@ -19,34 +20,101 @@ def remove_old_vcf():
         os.remove(filepath)
     vcfrem=glob.glob('input/input/*.vcf')    
     for filepath in vcfrem:
-        os.remove(filepath)  
-
+        os.remove(filepath)
+          
 def show_pdf(file_path):
     with open(file_path,"rb") as f:
         base64_pdf = base64.b64encode(f.read()).decode('utf-8')
     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)
 
+#@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):
+    for j in np.arange(0,len(to_dl_sbs)):
+        download_link1 = f'<a href="data:application/octet-stream;base64, \
+                {base64.b64encode(to_dl_sbs[j]).decode()}" download=" \
+                {file_to_lookat[j].name}SBS.pdf">Download {file_to_lookat[j].name} Single Base Substition pdf</a>'
+        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>'        
+        #download_link3 = f'<a href="data:application/octet-stream;base64, \
+        #        {base64.b64encode(to_dl_indel[j]).decode()}" download=" \
+        #        {file_to_lookat[j].name}Indel.pdf">Download {file_to_lookat[j].name} indel pdf</a>'
+        #download_link4 = f'<a href="data:application/octet-stream;base64, \
+        #        {base64.b64encode(to_dl_indel_text[j]).decode()}" download=" \
+        #        {file_to_lookat[j].name}Indel.txt">Download {file_to_lookat[j].name} indel table</a>'        
+        #download_link5 = f'<a href="data:application/octet-stream;base64, \
+        #        {base64.b64encode(to_dl_dbs[j]).decode()}" download=" \
+        #        {file_to_lookat[j].name}DBS.pdf">Download {file_to_lookat[j].name} Double Base Substitution pdf</a>'       
+        #download_link6 = f'<a href="data:application/octet-stream;base64, \
+        #        {base64.b64encode(to_dl_dbs_text[j]).decode()}" download=" \
+        #        {file_to_lookat[j].name}DBS.txt">Download {file_to_lookat[j].name} Double Base Substitution table</a>'        
+     
+        st.markdown(download_link1, unsafe_allow_html=True)
+
+        st.markdown(download_link2, unsafe_allow_html=True)
+
+        #st.markdown(download_link3, unsafe_allow_html=True)
+    
+        #st.markdown(download_link4, unsafe_allow_html=True)
+
+        #st.markdown(download_link5, unsafe_allow_html=True)
+
+        #st.markdown(download_link6, unsafe_allow_html=True)
+        #st.download_button(label="Download image with single base substitution profiles", key=j,
+        #                    data=to_dl_sbs[j],
+        #                    file_name="SBS.pdf",
+        #                    mime='application/octet-stream')
+        #st.download_button(label="Download image with indel profiles", key=0.5+j,
+        #                    data=to_dl_indel[j],
+        #                    file_name="idel.pdf",
+        #                    mime='application/octet-stream')
 
-def dl(file_vcf):
+
+
+def dl(valforkey):
+    #breakpoint()
     seev=glob.glob('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/*pdf')
     for i in seev:
         st.write('pdf file with sbs96 output is here: '+i)
     with open("output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf", "rb") as pdf_file:
-        PDFbyte1 = pdf_file.read()
-        st.download_button(label="Download image with single base substitution profiles", key='1',
-                            data=PDFbyte1,
-                            file_name="SBS.pdf",
-                            mime='application/octet-stream')
+        PDFbyte1 = pdf_file.read()    
+    with open("output/SBS96/Samples.txt","rb") as txt_file:
+        Txtbyte1 = txt_file.read()   
+        #st.download_button(label="Download image with single base substitution profiles", key=valforkey,
+        #                    data=PDFbyte1,
+        #                    file_name="SBS.pdf",
+        #                    mime='application/octet-stream')
 
-
-    with open("output/ID83/Suggested_Solution/COSMIC_ID83_Decomposed_Solution/ID83_Decomposition_Plots.pdf", "rb") as pdf_file:
-        PDFbyte2 = pdf_file.read()
-        st.download_button(label="Download image with indel profiles", key='2',
-                            data=PDFbyte2,
-                            file_name="idel.pdf",
-                            mime='application/octet-stream')
-    return file_vcf
+    
+    #with open("output/ID83/Suggested_Solution/COSMIC_ID83_Decomposed_Solution/ID83_Decomposition_Plots.pdf", "rb") as pdf_file:
+    #    PDFbyte2 = pdf_file.read()
+    PDFbyte2=[]
+    #with open("output/ID83/Samples.txt","rb") as txt_file:
+    #    Txtbyte2 = txt_file.read()  
+    Txtbyte2=[]
+    #with open("output/DBS78/Suggested_Solution/COSMIC_DBS78_Decomposed_Solution/DBS78_Decomposition_Plots.pdf", "rb") as pdf_file:
+    #    PDFbyte3 = pdf_file.read()
+    PDFbyte3 =[]
+    #with open("output/DBS78/Samples.txt","rb") as txt_file:
+    #    Txtbyte3 = txt_file.read() 
+    Txtbyte3=[]
+    os.system('rm -r output')  
+    os.system('rm -r input')       
+    #os.remove("output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf")
+    #os.remove("output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/*")
+    #os.remove("output/SBS96/Samples.txt")
+    #os.remove("output/ID83/Suggested_Solution/COSMIC_ID83_Decomposed_Solution/ID83_Decomposition_Plots.pdf")
+    #os.remove("output/ID83/Samples.txt")
+    #os.remove("output/DBS78/Suggested_Solution/COSMIC_DBS78_Decomposed_Solution/DBS78_Decomposition_Plots.pdf")
+    #os.remove("output/DBS78/Samples.txt")
+
+
+        #st.download_button(label="Download image with indel profiles", key=0.5+valforkey,
+        #                    data=PDFbyte2,
+        #                    file_name="idel.pdf",
+        #                    mime='application/octet-stream')
+    return PDFbyte1,PDFbyte2,PDFbyte3,Txtbyte1,Txtbyte2,Txtbyte3  
 
 
 
@@ -64,7 +132,7 @@ with st.form('get signature'):
 
 if file_to_lookat !=[] and sub:    
     #if st.button('get reference genome'):
-    st.write(os.path.dirname(SigProfilerMatrixGenerator.__file__))
+    #st.write(os.path.dirname(SigProfilerMatrixGenerator.__file__))
     dirtest=os.path.dirname(SigProfilerMatrixGenerator.__file__)
     
     #st.write(sys.path)
@@ -78,36 +146,54 @@ if file_to_lookat !=[] and sub:
                 #    st.write(i)
         ##genInstall.install('GRCh37')
     
-    if not os.path.exists('input'):
-        os.mkdir('input')
-    
-    if not os.path.exists('input/input'):
-        os.mkdir('input/input')
-
-    remove_old_vcf()
-
-
-    bytes_data=file_to_lookat[0].read()
-    with open(os.path.join("input",file_to_lookat[0].name),"wb") as f:
-        f.write(bytes_data)
-        f.close()
-        seev=glob.glob('input/*')
-        for i in seev:
-            st.write(i)
-    #vcfuse=glob.glob('file_to_lookat[0].name')[0]
-    #shutil.copy2(vcfuse,'input/'+vcfuse)
-    #pdb.set_trace()
-        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'):               
-    dl(file_to_lookat)
-   
-  #show_pdf('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf')
 
 
+    
+    to_dl_sbs=[]
+    to_dl_indel=[]
+    to_dl_dbs=[]
+    to_dl_sbs_text=[]
+    to_dl_indel_text=[]
+    to_dl_dbs_text=[]    
+    for j in np.arange(0,len(file_to_lookat)):
+        if not os.path.exists('input'):
+            os.mkdir('input')
+    
+        if not os.path.exists('input/input'):
+            os.mkdir('input/input')
+        remove_old_vcf()    
+        bytes_data=file_to_lookat[j].read()
+        with open(os.path.join("input",file_to_lookat[j].name),"wb") as f:
+            f.write(bytes_data)
+            f.close()
+            seev=glob.glob('input/*')
+            #for i in seev:
+            #    st.write(i)
+        #vcfuse=glob.glob('file_to_lookat[0].name')[0]
+        #shutil.copy2(vcfuse,'input/'+vcfuse)
+        #pdb.set_trace()
+            
+            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=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)
+      
+        #show_pdf('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf')
+
+
+
+            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)         
     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=3000,width=800)
-    remove_old_vcf() 
+    #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)