Update app.py

app.py

@@ -30,6 +30,9 @@ def show_pdf(file_path):
 
 @st.experimental_memo(suppress_st_warning=True)
 def dl(file_vcf):
+    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',
@@ -49,31 +52,38 @@ def dl(file_vcf):
 
 
 #st.write(glob.glob(os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/*txt')))
-
-if glob.glob(os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/*txt')) == []:
-    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)
+with st.form('get signature'):
+    if glob.glob(os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/chromosomes/tsb/GRCh37/')+'*txt') == []:
+        st.write('There is no reference genome, we need to download this')
+        refdownload=True
+    file_to_lookat=st.file_uploader('VCF upload here',type=[".vcf"],accept_multiple_files=True)
+    remove_old_vcf()
+    sub=st.form_submit_button('submit input')
+    
+if sub and file_to_lookat !=[]::    
+    #if st.button('get reference genome'):
+    st.write(os.path.dirname(SigProfilerMatrixGenerator.__file__))
+    dirtest=os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/chromosomes/tsb/GRCh37/')+'*txt'
+    st.write(dirtest)
+    #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(dirtest)
+            for i in seev:
+                st.write(i)
         ##genInstall.install('GRCh37')
 
-if not os.path.exists('input'):
-    os.mkdir('input')
+    if not os.path.exists('input'):
+        os.mkdir('input')
+    
+    if not os.path.exists('input/input'):
+        os.mkdir('input/input')
+
 
-if not os.path.exists('input/input'):
-    os.mkdir('input/input')
 
-file_to_lookat=st.file_uploader('VCF upload here',type=[".vcf"],accept_multiple_files=True)
-remove_old_vcf()
 
-if file_to_lookat !=[]:
     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)