如何比较两个不同文件中的两列，并为多个连续列添加从file2到file1的列

时间：2016-11-10 08:50:53

标签： bash unix awk

编码和使用awk相对较新，所以如果这是一个愚蠢的问题我很抱歉！ 我需要将文件1中的$ 3与文件2中的$ 3进行比较，如果它们匹配，则从文件1中打印行，并在文件2中使用相应的行条目10美元。我有一个执行此操作的命令，

awk 'NR==FNR{a[$3]=$10; next} a[$3] {print $0 "\t" a[$3]}' file2 file1

但是，file2的列数为$ 10- $ 647，我需要为所有637列执行上述操作。有没有办法循环这个？

示例文件1：

 1  715348  rs3131984   T   G   100 PASS    AC=5008;AF=1;AN=5008;NS=2504;DP=16986;EAS_AF=1;AMR_AF=1;AFR_AF=1;EUR_AF=1;SAS_AF=1;AA=.|||;VT=SNP   GT  1|1 1|1 1|1
 1  723798  rs34882115  CAG C   100 PASS    AC=4012;AF=0.801118;AN=5008;NS=2504;DP=24752;EAS_AF=0.7946;AMR_AF=0.8775;AFR_AF=0.5416;EUR_AF=0.9602;SAS_AF=0.9407;VT=INDEL GT  1|1 1|1 1|1
 1  723891  rs2977670   G   C   100 PASS    AC=3906;AF=0.779952;AN=5008;NS=2504;DP=22718;EAS_AF=0.7917;AMR_AF=0.8689;AFR_AF=0.4849;EUR_AF=0.9483;SAS_AF=0.9305;AA=.|||;VT=SNP   GT  1|1 1|1 1|1
 1  729679  rs4951859   C   G   100 PASS    AC=3205;AF=0.639976;AN=5008;NS=2504;DP=18762;EAS_AF=0.6875;AMR_AF=0.7536;AFR_AF=0.2905;EUR_AF=0.841;SAS_AF=0.7761;AA=.|||;VT=SNP    GT  1|0 1|1 1|0
 1  752566  rs3094315   G   A   100 PASS    AC=3597;AF=0.718251;AN=5008;NS=2504;DP=21293;EAS_AF=0.8839;AMR_AF=0.804;AFR_AF=0.3873;EUR_AF=0.84;SAS_AF=0.8088;AA=.|||;VT=SNP  GT  0|1 1|1 0|1
 1  752721  rs3131972   A   G   100 PASS    AC=3272;AF=0.653355;AN=5008;NS=2504;DP=22729;EAS_AF=0.7659;AMR_AF=0.7363;AFR_AF=0.2905;EUR_AF=0.839;SAS_AF=0.7781;AA=.|||;VT=SNP    GT  0|1 1|1 0|1
 1  754182  rs3131969   A   G   100 PASS    AC=3398;AF=0.678514;AN=5008;NS=2504;DP=16315;EAS_AF=0.7331;AMR_AF=0.7565;AFR_AF=0.3525;EUR_AF=0.8718;SAS_AF=0.8088;AA=.|||;VT=SNP   GT  0|1 1|1 0|1
 1  754192  rs3131968   A   G   100 PASS    AC=3398;AF=0.678514;AN=5008;NS=2504;DP=16981;EAS_AF=0.7331;AMR_AF=0.7565;AFR_AF=0.3525;EUR_AF=0.8718;SAS_AF=0.8088;AA=.|||;VT=SNP   GT  0|1 1|1 0|1
 1  754334  rs3131967   T   C   100 PASS    AC=3427;AF=0.684305;AN=5008;NS=2504;DP=21917;EAS_AF=0.7629;AMR_AF=0.755;AFR_AF=0.3525;EUR_AF=0.8718;SAS_AF=0.8088;AA=.|||;VT=SNP    GT  0|1 1|1 0|1
 1  754503  rs3115859   G   A   100 PASS    AC=3325;AF=0.663938;AN=5008;NS=2504;DP=19944;EAS_AF=0.7629;AMR_AF=0.7378;AFR_AF=0.3374;EUR_AF=0.839;SAS_AF=0.771;AA=.|||;VT=SNP GT  0|1 1|1 0|1
 1  754964  rs3131966   C   T   100 PASS    AC=3322;AF=0.663339;AN=5008;NS=2504;DP=19476;EAS_AF=0.7629;AMR_AF=0.7378;AFR_AF=0.3366;EUR_AF=0.837;SAS_AF=0.771;AA=.|||;VT=SNP GT  0|1 1|1 0|1
 1  755887  rs3131964   C   G   100 PASS    AC=4905;AF=0.979433;AN=5008;NS=2504;DP=22796;EAS_AF=1;AMR_AF=0.9914;AFR_AF=0.9304;EUR_AF=0.995;SAS_AF=1;AA=.|||;VT=SNP  GT  1|1 1|1 1|1
 1  755890  rs3115858   A   T   100 PASS    AC=3763;AF=0.751398;AN=5008;NS=2504;DP=23185;EAS_AF=0.8839;AMR_AF=0.8242;AFR_AF=0.4539;EUR_AF=0.8728;SAS_AF=0.8405;AA=.|||;VT=SNP   GT  0|1 1|1 0|1
 1  756604  rs3131962   A   G   100 PASS    AC=3746;AF=0.748003;AN=5008;NS=2504;DP=28270;EAS_AF=0.8829;AMR_AF=0.8242;AFR_AF=0.4501;EUR_AF=0.8698;SAS_AF=0.8323;AA=.|||;VT=SNP   GT  0|1 1|1 0|1

示例文件2：

1   742429  rs3094315   A   G   .   .   .   GT  0/0 0/0
1   1011278 rs3737728   G   A   .   .   .   GT  0/0 0/1
1   1077546 rs9442380   C   T   .   .   .   GT  0/0 0/0
1   1084601 rs4970362   G   A   .   .   .   GT  0/0 0/1
1   1089205 rs9660710   C   A   .   .   .   GT  0/0 0/0
1   1300787 rs2765033   C   T   .   .   .   GT  0/0 0/1
1   756604  rs3131962   A   G   100 PASS    AC=3746;AF=0.748003;AN=5008;NS=2504;DP=28270;EAS_AF=0.8829;AMR_AF=0.8242;AFR_AF=0.4501;EUR_AF=0.8698;SAS_AF=0.8323;AA=.|||;VT=SNP   GT  0|1 1|1
1   1303878 rs2649588   T   C   .   .   .   GT  0/0 0/1
1   1695996 rs6603811   C   T   .   .   .   GT  0/0 0/0
1   1782971 rs10907192  G   A   .   .   .   GT  0/0 0/0
1   1878053 rs3820011   C   A   .   .   .   GT  0/1 0/1
1   1882185 rs2803291   C   T   .   .   .   GT  0/0 0/0

awk是最好的方法吗？我不确定如何制作任何类型的循环。非常感谢所有帮助和解释！

2 个答案:

答案 0 :(得分：0)

我愿意：

$ column_file1=`awk '{print NF}' file1 | tail -1`
$ paste file1 file2 | awk -v c1=column_file1 '{if($3==$(3+c1)){for(i=1;i<=647;i++)if(i<=c1 || i>c1+10){printf "%s ", $i}; printf "\n"}}'

paste只需逐行加入这两个文件。

awk中的第一个if检查两个文件的第三个字段是否匹配（现在考虑，第二个文件的第一个字段只是$(1+c1)）。如果条件为真，则输入一个打印（在同一行 - printf "%s ", $i - ）所有字段的循环，避开第二个文件的前10个（if(i<=c1 || i>c1+10)）。一旦循环结束（所以你打印了所有的线）转到新线。如果文件结构良好（每个字段具有相同的宽度），则可以使用print $0并将输出通过管道传输到colrm。

如果您喜欢只使用awk

将以下内容复制到文件中

#!/bin/awk -f

{if(NR == FNR)
    {
        a[$3] = $10;
        for(i=11;i<=647;i++){
            a[$3] = a[$3] "\t" $i
        };
        next
    }
    else{
        if($3 in a){print $0 "\t" a[$3]}
    }
}

然后用

运行它 
$ awk -f <name_of_file> file2 file1

告诉我你是否有问题

修改

我在第一个例子中忘记了tail -1。这适用于您提供的示例。

答案 1 :(得分：-1)

试试这个 -

FILE1.TXT 

    #cat file1.txt
    1 715348  rs3131984   T   G   100 PASS    AC=5008;AF=1;AN=5008;NS=2504;DP=16986;EAS_AF=1;AMR_AF=1;AFR_AF=1;EUR_AF=1;SAS_AF=1;AA=.|||;VT=SNP   GT  1|1 1|1 1|1
    1 723798  rs34882115  CAG C   100 PASS    AC=4012;AF=0.801118;AN=5008;NS=2504;DP=24752;EAS_AF=0.7946;AMR_AF=0.8775;AFR_AF=0.5416;EUR_AF=0.9602;SAS_AF=0.9407;VT=INDEL GT  1|1 1|1 1|1
    1 723891  rs2977670   G   C   100 PASS    AC=3906;AF=0.779952;AN=5008;NS=2504;DP=22718;EAS_AF=0.7917;AMR_AF=0.8689;AFR_AF=0.4849;EUR_AF=0.9483;SAS_AF=0.9305;AA=.|||;VT=SNP   GT  1|1 1|1 1|1
    1 729679  rs4951859   C   G   100 PASS    AC=3205;AF=0.639976;AN=5008;NS=2504;DP=18762;EAS_AF=0.6875;AMR_AF=0.7536;AFR_AF=0.2905;EUR_AF=0.841;SAS_AF=0.7761;AA=.|||;VT=SNP    GT  1|0 1|1 1|0
    1 752566  rs3094315   G   A   100 PASS    AC=3597;AF=0.718251;AN=5008;NS=2504;DP=21293;EAS_AF=0.8839;AMR_AF=0.804;AFR_AF=0.3873;EUR_AF=0.84;SAS_AF=0.8088;AA=.|||;VT=SNP  GT  0|1 1|1 0|1
    1 752721  rs3131972   A   G   100 PASS    AC=3272;AF=0.653355;AN=5008;NS=2504;DP=22729;EAS_AF=0.7659;AMR_AF=0.7363;AFR_AF=0.2905;EUR_AF=0.839;SAS_AF=0.7781;AA=.|||;VT=SNP    GT  0|1 1|1 0|1
    1 754182  rs3131969   A   G   100 PASS    AC=3398;AF=0.678514;AN=5008;NS=2504;DP=16315;EAS_AF=0.7331;AMR_AF=0.7565;AFR_AF=0.3525;EUR_AF=0.8718;SAS_AF=0.8088;AA=.|||;VT=SNP   GT  0|1 1|1 0|1
    1 754192  rs3131968   A   G   100 PASS    AC=3398;AF=0.678514;AN=5008;NS=2504;DP=16981;EAS_AF=0.7331;AMR_AF=0.7565;AFR_AF=0.3525;EUR_AF=0.8718;SAS_AF=0.8088;AA=.|||;VT=SNP   GT  0|1 1|1 0|1
    1 754334  rs3131967   T   C   100 PASS    AC=3427;AF=0.684305;AN=5008;NS=2504;DP=21917;EAS_AF=0.7629;AMR_AF=0.755;AFR_AF=0.3525;EUR_AF=0.8718;SAS_AF=0.8088;AA=.|||;VT=SNP    GT  0|1 1|1 0|1
    1 754503  rs3115859   G   A   100 PASS    AC=3325;AF=0.663938;AN=5008;NS=2504;DP=19944;EAS_AF=0.7629;AMR_AF=0.7378;AFR_AF=0.3374;EUR_AF=0.839;SAS_AF=0.771;AA=.|||;VT=SNP GT  0|1 1|1 0|1
    1 754964  rs3131966   C   T   100 PASS    AC=3322;AF=0.663339;AN=5008;NS=2504;DP=19476;EAS_AF=0.7629;AMR_AF=0.7378;AFR_AF=0.3366;EUR_AF=0.837;SAS_AF=0.771;AA=.|||;VT=SNP GT  0|1 1|1 0|1
    1 755887  rs3131964   C   G   100 PASS    AC=4905;AF=0.979433;AN=5008;NS=2504;DP=22796;EAS_AF=1;AMR_AF=0.9914;AFR_AF=0.9304;EUR_AF=0.995;SAS_AF=1;AA=.|||;VT=SNP  GT  1|1 1|1 1|1
    1 755890  rs3115858   A   T   100 PASS    AC=3763;AF=0.751398;AN=5008;NS=2504;DP=23185;EAS_AF=0.8839;AMR_AF=0.8242;AFR_AF=0.4539;EUR_AF=0.8728;SAS_AF=0.8405;AA=.|||;VT=SNP   GT  0|1 1|1 0|1
    1 756604  rs3131962   A   G   100 PASS    AC=3746;AF=0.748003;AN=5008;NS=2504;DP=28270;EAS_AF=0.8829;AMR_AF=0.8242;AFR_AF=0.4501;EUR_AF=0.8698;SAS_AF=0.8323;AA=.|||;VT=SNP   GT  0|1 1|1 0|1

FILE2.TXT 

#cat file2.txt
1   742429  rs3094315   A   G   .   .   .   GT  0/0 0/0
1   1011278 rs3737728   G   A   .   .   .   GT  0/0 0/1
1   1077546 rs9442380   C   T   .   .   .   GT  0/0 0/0
1   1084601 rs4970362   G   A   .   .   .   GT  0/0 0/1
1   1089205 rs9660710   C   A   .   .   .   GT  0/0 0/0
1   1300787 rs2765033   C   T   .   .   .   GT  0/0 0/1
1   756604  rs3131962   A   G   100 PASS    AC=3746;AF=0.748003;AN=5008;NS=2504;DP=28270;EAS_AF=0.8829;AMR_AF=0.8242;AFR_AF=0.4501;EUR_AF=0.8698;SAS_AF=0.8323;AA=.|||;VT=SNP   GT  0|1 1|1
1   1303878 rs2649588   T   C   .   .   .   GT  0/0 0/1
1   1695996 rs6603811   C   T   .   .   .   GT  0/0 0/0
1   1782971 rs10907192  G   A   .   .   .   GT  0/0 0/0
1   1878053 rs3820011   C   A   .   .   .   GT  0/1 0/1
1   1882185 rs2803291   C   T   .   .   .   GT  0/0 0/0

加入 - 

#awk 'NR==FNR {val[$3]=$10;next;} $3 in val {print $0,val[$3]}' file2.txt file1.txt
1 752566  rs3094315   G   A   100 PASS    AC=3597;AF=0.718251;AN=5008;NS=2504;DP=21293;EAS_AF=0.8839;AMR_AF=0.804;AFR_AF=0.3873;EUR_AF=0.84;SAS_AF=0.8088;AA=.|||;VT=SNP  GT  0|1 1|1 0|1 0/0
1 756604  rs3131962   A   G   100 PASS    AC=3746;AF=0.748003;AN=5008;NS=2504;DP=28270;EAS_AF=0.8829;AMR_AF=0.8242;AFR_AF=0.4501;EUR_AF=0.8698;SAS_AF=0.8323;AA=.|||;VT=SNP   GT  0|1 1|1 0|1 0|1
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