Update app.py

app.py

@@ -175,15 +175,17 @@ if file_to_lookat !=[] and sub:
     dirtest=os.path.dirname(SigProfilerMatrixGenerator.__file__)
     
     #st.write(sys.path)
-    if refdownload==True and referencegenome=='hg19':
-        
+    if refdownload==True:
+        if referencegenome=='GRCh38':
+            st.write('using liftover with hg19 instead of downloading Grch38')
         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')
+    #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)
@@ -230,19 +232,21 @@ if file_to_lookat !=[] and sub:
             tovcf['alt']=table_of_penn_file['Alt']
             nameuse=re.sub('xlsx$','vcf',file_to_lookat[j].name)
             tovcf.to_csv(nameuse,sep='\t',header=False, index=False)
+            st.write('original file read as:')
             st.write(table_of_penn_file)
-            st.write(tovcf)
-            st.write(nameuse)
+            #st.write(tovcf)
+            #st.write(nameuse)
             with open(nameuse,"rb") as txt_file:
                 bytes_data=txt_file.read()
             txt_file.close()
             with open(os.path.join("input",nameuse),"wb") as f:
+                st.write('file after liftover:')
                 st.write(os.path.join("input",nameuse))
                 f.write(bytes_data)
             f.close()
             seev=glob.glob('input/*')        
 
-            st.write(pd.read_csv(os.path.join("input",nameuse)    ))
+            #st.write(pd.read_csv(os.path.join("input",nameuse)    ))
         #vcfuse=glob.glob('file_to_lookat[0].name')[0]
         #shutil.copy2(vcfuse,'input/'+vcfuse)
         #pdb.set_trace()
@@ -252,7 +256,7 @@ if file_to_lookat !=[] and sub:
             
     
         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,dummary_id,summary_dbs=dl(j)
+            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)