xlsites.py 文件源码

def _second_start(read, poss, strand, chrom, segmentation, holesize_th):
    """
    Return the coordinate of second start.

    If read is not split or we wish algorithm
    to think of read as linear, second_start equals to 0.
    """
    holes = [j - i - 1 for i, j in zip(poss, poss[1:])]
    # Get the size of the biggest hole:
    biggest_hole_size = max(holes) if holes else 0

    second_start = 0
    is_strange = False
    if not segmentation:
        # Effectively this means, that read is considered as it has no holes.
        if biggest_hole_size > holesize_th:
            # Still, read is not treated as on with distinct second_start.
            # However, it is reported as starnge:
            is_strange = True
    else:
        biggest_hole_size_index = holes.index(biggest_hole_size)
        # Take right border of hole on "+" and left border on "-" strand:
        if strand == '+':
            second_start = poss[biggest_hole_size_index + 1]
        else:
            second_start = poss[biggest_hole_size_index]

        # Read is strange if:
        # it is not intersecting with segmentation AND
        # if there actually is a hole
        if not _intersects_with_annotaton(second_start, segmentation, chrom, strand) and \
                biggest_hole_size != 0:
            is_strange = True

    return second_start, is_strange