default.py 文件源码

def readBAM(BAMFile, contigs):
    """
    Parses an aligned BAM file for coverage.

    Args:
        BAMFile: The BAM file to parse.
        contigs: List of sidr.common.Contigs taken from input FASTA.
    Returns:
        contigs: Input contigs updated with coverage, measured as an
                 average over the whole contig.
    """
    alignment = pysam.AlignmentFile(BAMFile, "rb")
    click.echo("Reading BAM file")
    with click.progressbar(contigs) as ci:
        for contig in ci:
            covArray = [] # coverage over contig = sum(coverage per base)/number of bases
            for pile in alignment.pileup(region=str(contig)):
                covArray.append(pile.nsegments)
            try:
                contigs[contig].variables["Coverage"] = (sum(covArray) / len(covArray))
            except ZeroDivisionError: # should only occur if 0 coverage recorded
                contigs[contig].variables["Coverage"] = 0
    return contigs