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awk 匹配来自两个文件的三列并将匹配的行附加到新文件

[英]awk match three columns from two files and append matching lines to a new file

 原文  2021-10-28 16:26:34  5   2    linux/ awk

问题描述

There are many posts that are similar to this one.有很多帖子与此类似。 Hours into trouble shooting this I'm desperate, as it seems like it should be simple.解决这个问题的几个小时我很绝望，因为它看起来应该很简单。

I have one file that looks like this:我有一个看起来像这样的文件：

tig00000005 15310   16162   XP_012153921.1  NW_003797090.1  LOC105664333    PREDICTED: elastin-like
tig00000005 23339   23974   XP_012152584.1  NW_003797083.1  LOC100878991    PREDICTED: LOW QUALITY PROTEIN
tig00000005 24600   25138   XP_012143166.1  NW_003797196.1  LOC100881279    PREDICTED: ankyrin-2 isoform X2
tig00000005 2685    4511    XP_012144644.1  NW_003797249.1  LOC105662970    PREDICTED: fibrinogen alpha chain-like isoform X2
tig00000005 28923   29432   XP_012148395.1  NW_003797444.1  LOC100881617    PREDICTED: eukaryotic translation initiation factor 4 gamma 3-like isoform X12
tig00000005 32415   34324   XP_012153921.1  NW_003797090.1  LOC105664333    PREDICTED: elastin-like

And a second file that looks like this:还有一个看起来像这样的第二个文件：

tig00000005 maker   gene    15310   16162   .   +   .   ID=snap_masked-tig00000005-processed-gene-0.2;Name=snap_masked-tig00000005-processed-gene-0.2
tig00000005 maker   gene    16764   17237   .   +   .   ID=snap_masked-tig00000005-processed-gene-0.3;Name=snap_masked-tig00000005-processed-gene-0.3
tig00000005 maker   gene    23339   23974   .   +   .   ID=snap_masked-tig00000005-processed-gene-0.4;Name=snap_masked-tig00000005-processed-gene-0.4
tig00000005 maker   gene    24600   25138   .   -   .   ID=snap_masked-tig00000005-processed-gene-0.10;Name=snap_masked-tig00000005-processed-gene-0.10
tig00000005 maker   gene    25472   26900   .   +   .   ID=snap_masked-tig00000005-processed-gene-0.5;Name=snap_masked-tig00000005-processed-gene-0.5

I would like to match the 1, 2, and 3 column in the first file with the 1, 4, and 5 in the second, and if they match, append the second file's data to the first file, like so:我想将第一个文件中的 1、2 和 3 列与第二个文件中的 1、4 和 5 相匹配，如果它们匹配，则将第二个文件的数据附加到第一个文件中，如下所示：

tig00000005 15310   16162   XP_012153921.1  NW_003797090.1  LOC105664333    PREDICTED: elastin-like tig00000005 maker   gene    15310   16162   .   +   .   ID=snap_masked-tig00000005-processed-gene-0.2;Name=snap_masked-tig00000005-processed-gene-0.2

Some example code that has not worked:一些不起作用的示例代码：

awk 'OFS="\t"; FS="\t"; NR==FNR{a[$1,$2,$3]=$0; next} (($1,$4,$5) in a){print $0,a[$0]}'  file 1 file 2

awk 'OFS="\t"; FS="\t"; NR==FNR{a[$1,$2,$3]=($1,$4,$5)} {print $0,a[$0]}' file 1 file 2

First outputs a file with every line from file 1 followed by (not appended) file 2, second code throws errors related to the = function.首先输出文件 1 中的每一行，然后是（未附加）文件 2，第二个代码抛出与 = 函数相关的错误。 I've tried any permutation of this I can imagine.我已经尝试了我能想象的任何排列。 Thank you for any help you can provide感谢您提供任何帮助

2 个解决方案

解决方案1
 0  2021-10-28 16:36:03

Like this?像这样？

awk 'NR==FNR{a[$1 $2 $3]=$0; next}; {if($1 $4 $5 in a){print a[$1 $4 $5],$0}}' file1 file2
tig00000005 15310   16162   XP_012153921.1  NW_003797090.1  LOC105664333    PREDICTED: elastin-like tig00000005 maker   gene    15310   16162   .   +   .   ID=snap_masked-tig00000005-processed-gene-0.2;Name=snap_masked-tig00000005-processed-gene-0.2
tig00000005 23339   23974   XP_012152584.1  NW_003797083.1  LOC100878991    PREDICTED: LOW QUALITY PROTEIN tig00000005 maker   gene    23339   23974   .   +   .   ID=snap_masked-tig00000005-processed-gene-0.4;Name=snap_masked-tig00000005-processed-gene-0.4
tig00000005 24600   25138   XP_012143166.1  NW_003797196.1  LOC100881279    PREDICTED: ankyrin-2 isoform X2 tig00000005 maker   gene    24600   25138   .   -   .   ID=snap_masked-tig00000005-processed-gene-0.10;Name=snap_masked-tig00000005-processed-gene-0.10

Ti write to a new file just do awk 'NR==FNR{a[$1 $2 $3]=$0; next}; {if($1 $4 $5 in a){print a[$1 $4 $5],$0}}' file1 file2 > file3 Ti 写入新文件只需执行awk 'NR==FNR{a[$1 $2 $3]=$0; next}; {if($1 $4 $5 in a){print a[$1 $4 $5],$0}}' file1 file2 > file3 awk 'NR==FNR{a[$1 $2 $3]=$0; next}; {if($1 $4 $5 in a){print a[$1 $4 $5],$0}}' file1 file2 > file3

解决方案2
 0  2021-10-28 22:04:01

A couple small changes to OP's first awk script:对 OP 的第一个awk脚本进行了一些小改动：

# old:

awk 'OFS="\t"; FS="\t"; NR==FNR{a[$1,$2,$3]=$0; next} (($1,$4,$5) in a){print $0,a[$0]}' file1 file2

# new - add BEGIN block, modify print statement:

awk 'BEGIN {FS=OFS="\t"} NR==FNR{a[$1,$2,$3]=$0; next} (($1,$4,$5) in a){print a[$1,$4,$5],$0}' file1 file2

The modified awk script generates:修改后的awk脚本生成：

tig00000005 15310   16162   XP_012153921.1  NW_003797090.1  LOC105664333    PREDICTED: elastin-like tig00000005 maker   gene    15310   16162   .   +   .   ID=snap_masked-tig00000005-processed-gene-0.2;Name=snap_masked-tig00000005-processed-gene-0.2
tig00000005 23339   23974   XP_012152584.1  NW_003797083.1  LOC100878991    PREDICTED: LOW QUALITY PROTEIN tig00000005 maker   gene    23339   23974   .   +   .   ID=snap_masked-tig00000005-processed-gene-0.4;Name=snap_masked-tig00000005-processed-gene-0.4
tig00000005 24600   25138   XP_012143166.1  NW_003797196.1  LOC100881279    PREDICTED: ankyrin-2 isoform X2 tig00000005 maker   gene    24600   25138   .   -   .   ID=snap_masked-tig00000005-processed-gene-0.10;Name=snap_masked-tig00000005-processed-gene-0.10

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