Update app.py

app.py

@@ -132,11 +132,13 @@ def dl(valforkey):
 
 #st.write(glob.glob(os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/*txt')))
 with st.form('get signature'):
-    if glob.glob(os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/chromosomes/tsb/GRCh37/')+'*txt') == []:
+    if glob.glob(os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/chromosomes/tsb/GRCh3[78]/')+'*txt') == []:
         st.write('There is no reference genome, we need to download this')
         refdownload=True
     else:
-        refdownload=False    
+        st.write('using reference from here:'+glob.glob(os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/chromosomes/tsb/GRCh3[78]/'))[0])
+        refdownload=False 
+    referencegenome =st.radio('reference',['hg19','GRCh38'])    
     file_to_lookat=st.file_uploader('VCF upload here',type=[".vcf"],accept_multiple_files=True)
     remove_old_vcf()
     
@@ -148,11 +150,15 @@ if file_to_lookat !=[] and sub:
     dirtest=os.path.dirname(SigProfilerMatrixGenerator.__file__)
     
     #st.write(sys.path)
-    if refdownload==True:
+    if refdownload==True and referencegenome=='hg19':
+        
         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)
+    elif refdownload==True and referencegenome=='GRCh38':
+        with st.spinner('downloading GRCh38 reference'):
+            genInstall.install('GRCh38')
                 #seev=glob.glob(dirtest+'/references/chromosomes/tsb/GRCh37/*txt')
                 #for i in seev:
                 #    st.write(i)