transcriptome.py 文件源码

def is_read_exonic(aligned_segments, exon_breaks, first_exon, last_exon, min_overlap_frac=0.5):
    for read_start, read_end, _ in aligned_segments:
        ex_idx = bisect.bisect(exon_breaks, read_start, lo=2*first_exon, hi=2*(last_exon+1)) - 1
        if ex_idx > 2*last_exon:
            # read is out of bounds
            return False
        elif ex_idx % 2 == 1:
            # read starts in an intron
            exon_start = exon_breaks[ex_idx+1]
            exon_end = exon_breaks[ex_idx+2]
        else:
            # read starts in an exon
            exon_start = exon_breaks[ex_idx]
            exon_end = exon_breaks[ex_idx+1]
        segment_exonic = overlaps(read_start, read_end, exon_start, exon_end, min_overlap_frac)
        if not segment_exonic:
            return False
    return True