Update app.py

app.py

@@ -13,6 +13,10 @@ import numpy as np
 import pandas as pd
 import base64
 import streamlit.components.v1 as components
+from liftover import get_lifter
+
+converter = get_lifter('hg38', 'hg19')
+
 
 curdir= os.getcwd()
 
@@ -214,6 +218,11 @@ if file_to_lookat !=[] and sub:
         else:
             table_of_penn_file=pd.read_excel(file_to_lookat[j])
             tovcf=pd.DataFrame()
+            table_of_penn_file=table_of_penn_file.iloc[1:,:]
+            tt=table_of_penn_file[['Chrom','Pos']].apply(lambda x: converter[x[0]][int(x[1])][0],axis=1)
+            table_of_penn_file['Chrom']= [a[0] for a in tt]
+            table_of_penn_file['Pos']= [a[1] for a in tt]
+
             tovcf['Chrom']=table_of_penn_file['Chrom']
             tovcf['Pos']=table_of_penn_file['Pos']
             tovcf['db']='.'
@@ -226,10 +235,10 @@ if file_to_lookat !=[] and sub:
             st.write(nameuse)
             with open(nameuse,"rb") as txt_file:
                 bytes_data=txt_file.read()
-                txt_file.close()
+            txt_file.close()
             with open(os.path.join("input",nameuse),"wb") as f:
                 f.write(bytes_data)
-                f.close()
+            f.close()
                 seev=glob.glob('input/*')        
             #for i in seev:
             #    st.write(i)