ancient_filter.py 文件源码

def filter_bam(input_file, output_file, downweight_number, ctot, gtoa):
    """
        Takes a bam file as input and weights the quality of the reads down.

        Need to ensure we write the header out :)

        Investigate pysam and look for a header,
        this should really help us understand how to get this bam filter working 
        and writing the bam files directly back out to the terminal.
    """
    bam = pysam.Samfile(input_file,'rb')
    bam_out = pysam.Samfile(output_file, 'wb',template=bam) 
    for line in bam:
        change_bases_c = None
        change_bases_t = None
        seq = line.seq
        qual = line.qual
        if(ctot):
            change_bases_c = [check_c_2_t(nuc) and i < downweight_number for i, nuc in enumerate(seq)]
        if(gtoa):
            change_bases_t = [check_g_2_a(nuc) and (len(seq)-i) <= downweight_number for i, nuc in enumerate(seq)]
        new_qual = downweight_quality(qual,change_bases_c, change_bases_t)
        line.qual = new_qual
        bam_out.write(line)