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!
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
修改强>
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