diff --git a/src/db_utils/frequency_scripts/create_n_fill_exon_frequency_file.py b/src/db_utils/frequency_scripts/create_n_fill_exon_frequency_file.py index 532113693f70e3f42c5f957ffd511c79527195a5..966106e6c820d79ce2f55d6c6b84fedab3887340 100644 --- a/src/db_utils/frequency_scripts/create_n_fill_exon_frequency_file.py +++ b/src/db_utils/frequency_scripts/create_n_fill_exon_frequency_file.py @@ -119,14 +119,20 @@ def compute_gene_orf_data(df: pd.DataFrame) -> pd.DataFrame: :return: """ df['id_gene'] = df['id_exon'].str.replace(r'_\d+', '') - gene_len = df[['id_gene', 'length']].groupby('id_gene').sum().reset_index() + df_exon = df.loc[(df['ft_type'] == "aa") & (df['ft'] == 'A'), :] + res = df_exon.groupby('id_exon').count()['length'].values + if np.max(res) != np.min(res) != 1: + msg = "On exon must be present only once !" + logging.exception(msg) + raise ValueError(msg) + gene_len = df_exon[['id_gene', 'length']].groupby('id_gene').sum()\ + .reset_index() df = pd.merge(df, gene_len, how='left', on="id_gene", suffixes=['_exon', '_gene']) df['new_freq'] = df['frequency'] * (df['length_exon'] / df['length_gene']) df_final = df[['id_gene', 'ft_type', 'ft', 'new_freq']].\ groupby(['id_gene', 'ft_type', 'ft']).sum().reset_index() df_final.rename(columns={"new_freq": 'frequency'}, inplace=True) - df_final['frequency'] = round(df_final['frequency'], 5) return df_final @@ -174,6 +180,8 @@ def create_or_load_freq_table(ps: int) -> Tuple[pd.DataFrame, pd.DataFrame]: else: df_gene = pd.read_csv(Config_freq.output_gene_file, sep="\t") HG19 = None + df_exon['frequency'] = round(df_exon['frequency'], 5) + df_gene['frequency'] = round(df_gene['frequency'], 5) return df_exon, df_gene