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[FIX] unexpected columns in FS report with --no-english #25

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[FIX] unexpected columns in FS report with --no-english #25

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7 changes: 4 additions & 3 deletions scripts/frameshift_deletions_checks
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Original file line number Diff line number Diff line change
Expand Up @@ -738,9 +738,6 @@ 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
Expand Down Expand Up @@ -961,6 +958,10 @@ 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
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