Hi-C Data Loader

def load_hic_matrix(hic_path):
    f = open(hic_path, "r")
    
    # Parse the header
    header = f.next()
    assert header[0] == "#"
    min_row, max_row, min_col, max_col = [int(x) for x in header[2:].split(" ")]
    
    # Create an empty matrix of n_fragments x n_fragments
    hic = np.zeros((max_col + 1, max_col + 1))
    
    # Fill in the values (symmetric)
    for l in f:
       interaction, chr1, row, chr2, column = [int(x) for x in l.split("\t")]
       assert chr1 == chr2  # cis data only
       hic[row, column] = hic[column, row] = interaction
    
    # Make sure that the matrix is symmetric
    assert np.all(hic == hic.T)
    
    return hic