bio_io.py 文件源码

def combine_vcfs(output_filename, input_vcf_filenames):
    tmp_filename = output_filename + ".tmp"

    for (i,fn) in enumerate(input_vcf_filenames):
        if i == 0:
            args = 'cat ' + fn
            subprocess.check_call(args + " > " + tmp_filename, shell=True)
        else:
            args = 'grep -v "^#" ' + fn
            ret = subprocess.call(args + " >> " + tmp_filename, shell=True)
            if ret == 2:
                raise Exception("grep call failed: " + args)

    # Sort and index the files
    tk_tabix.sort_vcf(tmp_filename, output_filename)
    tk_tabix.index_vcf(output_filename)

    os.remove(tmp_filename)