linux awk匹配两个文件中的三列，并将匹配的行附加到新文件

有一个文件，看起来像这样：

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

第二个文件看起来像这样：

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

希望将第一个文件中的1、2和3列与第二个文件中的1、4和5列进行匹配，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：

1 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

 

解决方法：

awk 'NR==FNR{a[$1" "$2" "$3]=$0; next}; {if($1" "$4" "$5 in a){print a[$1" "$4" "$5],$0}}' file1 file2

1 awk 'NR==FNR{a[$1" "$2" "$3]=$0; next}; {if($1" "$4" "$5 in a){print a[$1" "$4" "$5],$0}}' file1 file2
2 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
3 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
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

要写入新文件，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

posted @ 2025-01-13 15:47  元宵不如汤圆  阅读(52)  评论(0)    收藏  举报