awk 匹配來自兩個文件的三列並將匹配的行附加到新文件

Question

有很多帖子與此類似。 解決這個問題的幾個小時我很絕望，因為它看起來應該很簡單。

我有一個看起來像這樣的文件：

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

還有一個看起來像這樣的第二個文件：

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

我想將第一個文件中的 1、2 和 3 列與第二個文件中的 1、4 和 5 相匹配，如果它們匹配，則將第二個文件的數據附加到第一個文件中，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

一些不起作用的示例代碼：

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

首先輸出文件 1 中的每一行，然后是（未附加）文件 2，第二個代碼拋出與 = 函數相關的錯誤。 我已經嘗試了我能想象的任何排列。 感謝您提供任何幫助

Answer 1

像這樣？

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 寫入新文件只需執行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

Answer 2

對 OP 的第一個awk腳本進行了一些小改動：

# 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

修改后的awk腳本生成：

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