CNV_CNVnator.py 文件源码

def run_cnvnator(input_file,output_file):
    root = output_file[:-3] + 'root'
    # 1
    cnv_extract_bam(input_file,root,others)
    # 2
    chr_path = file_path + '/cnv/scaffold'
    path = chr_path
    if not os.path.exists(path):
        os.mkdir(path)
        for record in SeqIO.parse(ref_fa,'fasta'):
            SeqIO.write(record,path+'/'+record.id+'.fa','fasta')

    cnv_generate_hist(root,chr_path,bin_win,others)
    # 3
    cnv_statistics(root,bin_win,others)
    # 4
    cnv_partitioning(root,bin_win,others)
    # 5
    cnv_call(root,output_file,bin_win,others)