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python根据基因ID筛选fasta格式的序列

python根据基因ID筛选fasta格式的序列

作者: 蜡笔小生信 | 来源:发表于2020-06-28 22:31 被阅读0次
    新手笔记:

    1.注意变量格式化
    2.注意read.line()和read.lines()的区别,后者需要strip("\n")
    3.v.write同时出现两行就不能写入文件(原因未知)

    import sys
    
    with open(sys.argv[1]) as f:
            with open(sys.argv[2]) as g:
                    with open(sys.argv[3],"a") as v:
                            end = {}
                            a = str()
                            ab = str()
                            ac = {}
                            d = str()
                            for x in f.readlines():
                                    if(x.startswith(">")):
                                            a = x.strip("\n")
                                    else:
                                            b = x.strip("\n")
                                            ab = "{" +'"' + a +'"'+ ":" +'"'+ b +'"' + "}"
                                            ac = eval(ab)
                                            end.update(ac)
                            for i in g.readlines():
                                    d = ">" + i.strip("\n")
                                    if (d in end.keys()):
                                            v.write(str(d)+"\n"+ end[d] + "\n")
                                    else:
                                            continue
    

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