# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
# --------------------------------------------------------
# a script to help read norm file.
# --------------------------------------------------------

import numpy as np

def read_singlechromosome_norm(external_norm_file, n, cell_line, replace_nan = True):
    CHR_norm_File = external_norm_file
    CHR_norm_File = CHR_norm_File.replace('#(CHR)', 'chr'+str(n))
    CHR_norm_File = CHR_norm_File.replace('#(CELLLINE)', cell_line)

    raw = open(CHR_norm_File, 'r').readlines()
    
    norm = np.array(list(map(float, raw)))
    
    if replace_nan:
        norm[np.isnan(norm)] = 1

    return norm