consensus.py 文件源码

def load_metrics_from_db(db_path, tx_mode, aln_mode):
    """
    Loads the alignment metrics for the mRNA/CDS alignments of transMap/AugustusTM/TMR
    """
    session = tools.sqlInterface.start_session(db_path)
    metrics_table = tools.sqlInterface.tables[aln_mode][tx_mode]['metrics']
    metrics_df = tools.sqlInterface.load_metrics(metrics_table, session)
    # unstack flattens the long-form data structure
    metrics_df = metrics_df.set_index(['AlignmentId', 'classifier']).unstack('classifier')
    metrics_df.columns = [col[1] for col in metrics_df.columns]
    metrics_df = metrics_df.reset_index()
    cols = ['AlnCoverage', 'AlnGoodness', 'AlnIdentity', 'PercentUnknownBases']
    metrics_df[cols] = metrics_df[cols].apply(pd.to_numeric)
    metrics_df['OriginalIntrons'] = metrics_df['OriginalIntrons'].fillna('')
    metrics_df['OriginalIntrons'] = [list(map(int, x)) if len(x[0]) > 0 else [] for x in
                                     metrics_df['OriginalIntrons'].str.split(',').tolist()]
    metrics_df['OriginalIntronsPercent'] = metrics_df['OriginalIntrons'].apply(calculate_vector_support, resolve_nan=1)
    session.close()
    return metrics_df