From 0d2830ec3898ecedd28e28ddc583ee31d9a1fbcd Mon Sep 17 00:00:00 2001
From: mcarrara <19552826+mcarrara-bioinfo@users.noreply.github.com>
Date: Tue, 22 Aug 2023 18:17:32 +0200
Subject: [PATCH] [FIX] unexpected columns in FS report with --no-english

---
 scripts/frameshift_deletions_checks | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/scripts/frameshift_deletions_checks b/scripts/frameshift_deletions_checks
index 0582cad..7a07e11 100755
--- a/scripts/frameshift_deletions_checks
+++ b/scripts/frameshift_deletions_checks
@@ -754,9 +754,6 @@ def write_english_summary(df_temp):
         text_row='; '.join([s for s in [support_status, homopolymeric_status, pos_critical_status] if s])
         variant_diagnosis.append(text_row)
 
-    df_temp.pop('stop_mismatches')
-    df_temp.pop('aa_position')
-    df_temp.pop('stoploss_nt')
     df_temp['variant_position_english']=variant_position_english
     df_temp['variant_diagnosis']=variant_diagnosis
     return df_temp
@@ -977,6 +974,10 @@ def main():
     if args.english==True:
         print("adding english language")
         df= write_english_summary(df)
+    # cleanup of internal stop codon information
+    df.pop('stop_mismatches')
+    df.pop('aa_position')
+    df.pop('stoploss_nt')
 
 
     df.to_csv(args.outfile, sep='\t') # write to tsv-file