Convert to fastq with counts

def _prepare_inputs(ma_fn, bam_file, out_dir):
    """
    Convert to fastq with counts
    """
    fixed_fa = os.path.join(out_dir, "file_reads.fa")
    count_name =dict()
    with file_transaction(fixed_fa) as out_tx:
        with open(out_tx, 'w') as out_handle:
            with open(ma_fn) as in_handle:
                h = next(in_handle)
                for line in in_handle:
                    cols = line.split("\t")
                    name_with_counts = "%s_x%s" % (cols[0], sum(map(int, cols[2:])))
                    count_name[cols[0]] = name_with_counts
                    out_handle.write(">%s\n%s\n" % (name_with_counts, cols[1]))
    fixed_bam = os.path.join(out_dir, "align.bam")
    bam_handle = pysam.AlignmentFile(bam_file, "rb")
    with pysam.AlignmentFile(fixed_bam, "wb", template=bam_handle) as out_handle:
        for read in bam_handle.fetch():
            read.query_name = count_name[read.query_name]
            out_handle.write(read)

    return fixed_fa, fixed_bam