Update app.py

app.py

@@ -30,17 +30,19 @@ def show_pdf(file_path):
 
 
 
-if st.button('get reference genome'):
-    st.write(os.path.dirname(SigProfilerMatrixGenerator.__file__))
-    dirtest=os.path.dirname(SigProfilerMatrixGenerator.__file__)
-    #st.write(sys.path)
-    urllib.request.urlretrieve('https://dl.dropboxusercontent.com/s/et97ewsct862x7m/references.zip?dl=0','references.zip')
-    with zipfile.ZipFile('references.zip', 'r') as zip_ref:
-        zip_ref.extractall(dirtest)
-        seev=glob.glob('/home/appuser/venv/lib/python3.9/site-packages/SigProfilerMatrixGenerator/references/*')
-        for i in seev:
-            st.write(i)
-    ##genInstall.install('GRCh37')
+if glob.glob(os.path.dirname(SigProfilerMatrixGenerator.__file__)) == []:
+    if st.button('get reference genome'):
+        st.write(os.path.dirname(SigProfilerMatrixGenerator.__file__))
+        dirtest=os.path.dirname(SigProfilerMatrixGenerator.__file__)
+        #st.write(sys.path)
+        with st.spinner('downloading hg19 reference'):
+            urllib.request.urlretrieve('https://dl.dropboxusercontent.com/s/et97ewsct862x7m/references.zip?dl=0','references.zip')
+            with zipfile.ZipFile('references.zip', 'r') as zip_ref:
+                zip_ref.extractall(dirtest)
+                seev=glob.glob(os.path.join(dirtest,'references'))
+                for i in seev:
+                    st.write(i)
+        ##genInstall.install('GRCh37')
 
 if not os.path.exists('input'):
     os.mkdir('input')
@@ -63,9 +65,24 @@ if file_to_lookat !=[]:
     with st.spinner('computing signatures'):
         sig.sigProfilerExtractor("vcf", "output", "input", minimum_signatures=1, maximum_signatures=3)
    
-    show_pdf('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf')
+  #show_pdf('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf')
+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')
+
+
+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')
     
-    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() 
+        
+ 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()