Cannot create new percent columns from CSV file
Try using groupby with a custom function and apply.

df = pd.DataFrame()
df['RunNumber'] = ['Run1','Run1','Run2','Run2']
df['A']=[500,60,20,30]
df['B']=[5,5,2,2]
df['C']=[5,10,2,6]
df['D']=[3,4,5,4]
df['E']=[65,56,56,44]

def calculate_sum_percent(input_df):
    output_df = pd.Series()
    output_df['AB_sum']=input_df['A'].sum() + input_df['B'].sum()
    output_df['CD_sum']=input_df['C'].sum() + input_df['D'].sum()
    output_df['AB_perc']=100*(input_df['A'].sum() + input_df['B'].sum())/input_df.sum().sum()
    output_df['CD_perc']=100*(input_df['C'].sum() + input_df['D'].sum())/input_df.sum().sum()
    return output_df

stats_df = df.groupby('RunNumber').apply(calculate_sum_percent)
display(stats_df)