使用python的模块edlib,可实现要比较的两种变异的全局比对（mode=“HW”），
通过输入要比较的两种标记的ref，alt；分别获得对应的全局比对后的格式，然后再做比较。
比如：

image.png

import sys
import edlib

def diff(s, t):
    ref, alt = [], []
    flag = False
    if len(s) < len(t): flag, s, t = True, t, s
    t = t + " "*(len(s)-len(t))
    aln = edlib.align(s, t, mode="HW", task = "path")
    match = edlib.getNiceAlignment(aln, s, t)['matched_aligned']
#    print(match)
    path = len(match)
    for i in range(path):
        if match[i] == "|": continue
        elif match[i] == "." or match[i] == "-":
            ref.append(s[i]) 
            alt.append(t[i])
#    print(edlib.getNiceAlignment(aln, s, t))
    if flag:    
        a="".join(alt), "".join(ref)
    else:   
        a="".join(ref), "".join(alt)
    return a

with open('diff_clinv_dbsnp.xls', 'r') as multi_file:
    lines = multi_file.readlines()

with open('output.xls', 'w') as single_file:
    for line in lines:
        if line.startswith('V1'):
            single_file.write(line)
            continue

        columns = line.strip().split('\t')
        custom_cols = columns[:3]
        chromosome, position, ref_base, alt_base = columns[3:7]
        other_cols = columns[7:]
        ref1 = other_cols[0]
        alt1 = other_cols[1]
        glo = diff(ref_base,alt_base)
        clinvar = diff(ref1,alt1)
        if glo ==  clinvar:
            same_status = 'Y'
        else:
            same_status = 'N'
        single_file.write('\t'.join(custom_cols + [chromosome, str(int(position)), str(glo), str(clinvar), ref_base, alt_base] + other_cols + [same_status]) + '\n')