parse.py 文件源码

def read_cufflinks(sample_path, isoforms=False):
    ''' Function for reading a Cufflinks quantification result.

    Returns
    -------
    A pandas.Series with the expression values in the sample.
    '''
    if isoforms:
        quant_file = sample_path + '/isoforms.fpkm_tracking'
    else:
        quant_file = sample_path + '/genes.fpkm_tracking'
    df = pd.read_table(quant_file, engine='c',
                                   usecols=['tracking_id', 'FPKM'],
                                   index_col=0,
                                   dtype={'tracking_id': np.str, 'FPKM': np.float64})

    df['tracking_id'] = df.index
    df = df.groupby('tracking_id').sum()
    df['TPM'] = df['FPKM'] / df['FPKM'].sum() * 1e6

    df = df.rename(columns={'tracking_id': 'target_id'})
    return df['TPM']