Replacing matching entries in one column of a file by another column from a different file





.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty{ margin-bottom:0;
}







5















I have two tab-separated files which look as follows:



file1:



NC_008146.1     WP_011558474.1  1155234 1156286 44173
NC_008146.1 WP_011558475.1 1156298 1156807 12
NC_008146.1 WP_011558476.1 1156804 1157820 -3
NC_008705.1 WP_011558474.1 1159543 1160595 42748
NC_008705.1 WP_011558475.1 1160607 1161116 12
NC_008705.1 WP_011558476.1 1161113 1162129 -3
NC_009077.1 WP_011559727.1 2481079 2481633 8
NC_009077.1 WP_011854835.1 1163068 1164120 42559
NC_009077.1 WP_011854836.1 1164127 1164636 7


file2:



NC_008146.1     GCF_000014165.1_ASM1416v1_protein.faa
NC_008705.1 GCF_000015405.1_ASM1540v1_protein.faa
NC_009077.1 GCF_000016005.1_ASM1600v1_protein.faa


I want to match column 1 of file1 to file2 and replace itself with the respective column 2 entry of file 2.
The output would look like this:



GCF_000014165.1_ASM1416v1_protein.faa     WP_011558474.1  1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7









share|improve this question









New contributor




BhushanDhamale is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.





















  • It looks like you might also be interested in our sister site: Bioinformatics.

    – terdon
    14 hours ago











  • Thank you for the link @terdon!

    – BhushanDhamale
    14 hours ago


















5















I have two tab-separated files which look as follows:



file1:



NC_008146.1     WP_011558474.1  1155234 1156286 44173
NC_008146.1 WP_011558475.1 1156298 1156807 12
NC_008146.1 WP_011558476.1 1156804 1157820 -3
NC_008705.1 WP_011558474.1 1159543 1160595 42748
NC_008705.1 WP_011558475.1 1160607 1161116 12
NC_008705.1 WP_011558476.1 1161113 1162129 -3
NC_009077.1 WP_011559727.1 2481079 2481633 8
NC_009077.1 WP_011854835.1 1163068 1164120 42559
NC_009077.1 WP_011854836.1 1164127 1164636 7


file2:



NC_008146.1     GCF_000014165.1_ASM1416v1_protein.faa
NC_008705.1 GCF_000015405.1_ASM1540v1_protein.faa
NC_009077.1 GCF_000016005.1_ASM1600v1_protein.faa


I want to match column 1 of file1 to file2 and replace itself with the respective column 2 entry of file 2.
The output would look like this:



GCF_000014165.1_ASM1416v1_protein.faa     WP_011558474.1  1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7









share|improve this question









New contributor




BhushanDhamale is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.





















  • It looks like you might also be interested in our sister site: Bioinformatics.

    – terdon
    14 hours ago











  • Thank you for the link @terdon!

    – BhushanDhamale
    14 hours ago














5












5








5








I have two tab-separated files which look as follows:



file1:



NC_008146.1     WP_011558474.1  1155234 1156286 44173
NC_008146.1 WP_011558475.1 1156298 1156807 12
NC_008146.1 WP_011558476.1 1156804 1157820 -3
NC_008705.1 WP_011558474.1 1159543 1160595 42748
NC_008705.1 WP_011558475.1 1160607 1161116 12
NC_008705.1 WP_011558476.1 1161113 1162129 -3
NC_009077.1 WP_011559727.1 2481079 2481633 8
NC_009077.1 WP_011854835.1 1163068 1164120 42559
NC_009077.1 WP_011854836.1 1164127 1164636 7


file2:



NC_008146.1     GCF_000014165.1_ASM1416v1_protein.faa
NC_008705.1 GCF_000015405.1_ASM1540v1_protein.faa
NC_009077.1 GCF_000016005.1_ASM1600v1_protein.faa


I want to match column 1 of file1 to file2 and replace itself with the respective column 2 entry of file 2.
The output would look like this:



GCF_000014165.1_ASM1416v1_protein.faa     WP_011558474.1  1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7









share|improve this question









New contributor




BhushanDhamale is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.












I have two tab-separated files which look as follows:



file1:



NC_008146.1     WP_011558474.1  1155234 1156286 44173
NC_008146.1 WP_011558475.1 1156298 1156807 12
NC_008146.1 WP_011558476.1 1156804 1157820 -3
NC_008705.1 WP_011558474.1 1159543 1160595 42748
NC_008705.1 WP_011558475.1 1160607 1161116 12
NC_008705.1 WP_011558476.1 1161113 1162129 -3
NC_009077.1 WP_011559727.1 2481079 2481633 8
NC_009077.1 WP_011854835.1 1163068 1164120 42559
NC_009077.1 WP_011854836.1 1164127 1164636 7


file2:



NC_008146.1     GCF_000014165.1_ASM1416v1_protein.faa
NC_008705.1 GCF_000015405.1_ASM1540v1_protein.faa
NC_009077.1 GCF_000016005.1_ASM1600v1_protein.faa


I want to match column 1 of file1 to file2 and replace itself with the respective column 2 entry of file 2.
The output would look like this:



GCF_000014165.1_ASM1416v1_protein.faa     WP_011558474.1  1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7






awk






share|improve this question









New contributor




BhushanDhamale is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.











share|improve this question









New contributor




BhushanDhamale is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.









share|improve this question




share|improve this question








edited 14 hours ago









Rui F Ribeiro

41.9k1483142




41.9k1483142






New contributor




BhushanDhamale is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.









asked 15 hours ago









BhushanDhamaleBhushanDhamale

1503




1503




New contributor




BhushanDhamale is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.





New contributor





BhushanDhamale is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.






BhushanDhamale is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.













  • It looks like you might also be interested in our sister site: Bioinformatics.

    – terdon
    14 hours ago











  • Thank you for the link @terdon!

    – BhushanDhamale
    14 hours ago



















  • It looks like you might also be interested in our sister site: Bioinformatics.

    – terdon
    14 hours ago











  • Thank you for the link @terdon!

    – BhushanDhamale
    14 hours ago

















It looks like you might also be interested in our sister site: Bioinformatics.

– terdon
14 hours ago





It looks like you might also be interested in our sister site: Bioinformatics.

– terdon
14 hours ago













Thank you for the link @terdon!

– BhushanDhamale
14 hours ago





Thank you for the link @terdon!

– BhushanDhamale
14 hours ago










2 Answers
2






active

oldest

votes


















11














You can do this very easily with awk:



$ awk 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


Or, since that looks like a tab-separated file:



$ awk -vOFS="t" 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.



Explanation





  • NR==FNR : NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here, file2) is being read.


  • a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to the next line. This ensures the next block isn't executed for the 1st file.


  • {$1=a[$1]; print} : now, in the second file, set the 1st field to whatever value was saved in the array a for the 1st field (so, the associated value from file2) and print the resulting line.






share|improve this answer





















  • 1





    NR == FNR doesn't work correctly when the first file is empty. See this and the associated answer for a workaround

    – iruvar
    15 hours ago








  • 1





    @iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.

    – terdon
    14 hours ago













  • sorry I should have said in this particular case file2 and not file1 is empty. Sane behaviour when file2 is empty is to report the contents of file1. The problem with NR == FNR is that code associated with it executes on the contents of file1 when file2 is empty

    – iruvar
    14 hours ago






  • 1





    @iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.

    – terdon
    14 hours ago





















13














No need for awk, assuming the files are sorted, you can use coreutils join:



join -o '2.2 1.2 1.3 1.4 1.5' file1 file2


Output:



GCF_000014165.1_ASM1416v1_protein.faa     WP_011558474.1  1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:



join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)





share|improve this answer


























    Your Answer








    StackExchange.ready(function() {
    var channelOptions = {
    tags: "".split(" "),
    id: "106"
    };
    initTagRenderer("".split(" "), "".split(" "), channelOptions);

    StackExchange.using("externalEditor", function() {
    // Have to fire editor after snippets, if snippets enabled
    if (StackExchange.settings.snippets.snippetsEnabled) {
    StackExchange.using("snippets", function() {
    createEditor();
    });
    }
    else {
    createEditor();
    }
    });

    function createEditor() {
    StackExchange.prepareEditor({
    heartbeatType: 'answer',
    autoActivateHeartbeat: false,
    convertImagesToLinks: false,
    noModals: true,
    showLowRepImageUploadWarning: true,
    reputationToPostImages: null,
    bindNavPrevention: true,
    postfix: "",
    imageUploader: {
    brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
    contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
    allowUrls: true
    },
    onDemand: true,
    discardSelector: ".discard-answer"
    ,immediatelyShowMarkdownHelp:true
    });


    }
    });






    BhushanDhamale is a new contributor. Be nice, and check out our Code of Conduct.










    draft saved

    draft discarded


















    StackExchange.ready(
    function () {
    StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2funix.stackexchange.com%2fquestions%2f510709%2freplacing-matching-entries-in-one-column-of-a-file-by-another-column-from-a-diff%23new-answer', 'question_page');
    }
    );

    Post as a guest















    Required, but never shown

























    2 Answers
    2






    active

    oldest

    votes








    2 Answers
    2






    active

    oldest

    votes









    active

    oldest

    votes






    active

    oldest

    votes









    11














    You can do this very easily with awk:



    $ awk 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
    GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


    Or, since that looks like a tab-separated file:



    $ awk -vOFS="t" 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
    GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


    This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.



    Explanation





    • NR==FNR : NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here, file2) is being read.


    • a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to the next line. This ensures the next block isn't executed for the 1st file.


    • {$1=a[$1]; print} : now, in the second file, set the 1st field to whatever value was saved in the array a for the 1st field (so, the associated value from file2) and print the resulting line.






    share|improve this answer





















    • 1





      NR == FNR doesn't work correctly when the first file is empty. See this and the associated answer for a workaround

      – iruvar
      15 hours ago








    • 1





      @iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.

      – terdon
      14 hours ago













    • sorry I should have said in this particular case file2 and not file1 is empty. Sane behaviour when file2 is empty is to report the contents of file1. The problem with NR == FNR is that code associated with it executes on the contents of file1 when file2 is empty

      – iruvar
      14 hours ago






    • 1





      @iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.

      – terdon
      14 hours ago


















    11














    You can do this very easily with awk:



    $ awk 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
    GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


    Or, since that looks like a tab-separated file:



    $ awk -vOFS="t" 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
    GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


    This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.



    Explanation





    • NR==FNR : NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here, file2) is being read.


    • a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to the next line. This ensures the next block isn't executed for the 1st file.


    • {$1=a[$1]; print} : now, in the second file, set the 1st field to whatever value was saved in the array a for the 1st field (so, the associated value from file2) and print the resulting line.






    share|improve this answer





















    • 1





      NR == FNR doesn't work correctly when the first file is empty. See this and the associated answer for a workaround

      – iruvar
      15 hours ago








    • 1





      @iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.

      – terdon
      14 hours ago













    • sorry I should have said in this particular case file2 and not file1 is empty. Sane behaviour when file2 is empty is to report the contents of file1. The problem with NR == FNR is that code associated with it executes on the contents of file1 when file2 is empty

      – iruvar
      14 hours ago






    • 1





      @iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.

      – terdon
      14 hours ago
















    11












    11








    11







    You can do this very easily with awk:



    $ awk 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
    GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


    Or, since that looks like a tab-separated file:



    $ awk -vOFS="t" 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
    GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


    This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.



    Explanation





    • NR==FNR : NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here, file2) is being read.


    • a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to the next line. This ensures the next block isn't executed for the 1st file.


    • {$1=a[$1]; print} : now, in the second file, set the 1st field to whatever value was saved in the array a for the 1st field (so, the associated value from file2) and print the resulting line.






    share|improve this answer















    You can do this very easily with awk:



    $ awk 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
    GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


    Or, since that looks like a tab-separated file:



    $ awk -vOFS="t" 'NR==FNR{a[$1]=$2; next}{$1=a[$1]; print}' file2 file1
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
    GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


    This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.



    Explanation





    • NR==FNR : NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here, file2) is being read.


    • a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to the next line. This ensures the next block isn't executed for the 1st file.


    • {$1=a[$1]; print} : now, in the second file, set the 1st field to whatever value was saved in the array a for the 1st field (so, the associated value from file2) and print the resulting line.







    share|improve this answer














    share|improve this answer



    share|improve this answer








    edited 14 hours ago

























    answered 15 hours ago









    terdonterdon

    133k33268448




    133k33268448








    • 1





      NR == FNR doesn't work correctly when the first file is empty. See this and the associated answer for a workaround

      – iruvar
      15 hours ago








    • 1





      @iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.

      – terdon
      14 hours ago













    • sorry I should have said in this particular case file2 and not file1 is empty. Sane behaviour when file2 is empty is to report the contents of file1. The problem with NR == FNR is that code associated with it executes on the contents of file1 when file2 is empty

      – iruvar
      14 hours ago






    • 1





      @iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.

      – terdon
      14 hours ago
















    • 1





      NR == FNR doesn't work correctly when the first file is empty. See this and the associated answer for a workaround

      – iruvar
      15 hours ago








    • 1





      @iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.

      – terdon
      14 hours ago













    • sorry I should have said in this particular case file2 and not file1 is empty. Sane behaviour when file2 is empty is to report the contents of file1. The problem with NR == FNR is that code associated with it executes on the contents of file1 when file2 is empty

      – iruvar
      14 hours ago






    • 1





      @iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.

      – terdon
      14 hours ago










    1




    1





    NR == FNR doesn't work correctly when the first file is empty. See this and the associated answer for a workaround

    – iruvar
    15 hours ago







    NR == FNR doesn't work correctly when the first file is empty. See this and the associated answer for a workaround

    – iruvar
    15 hours ago






    1




    1





    @iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.

    – terdon
    14 hours ago







    @iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.

    – terdon
    14 hours ago















    sorry I should have said in this particular case file2 and not file1 is empty. Sane behaviour when file2 is empty is to report the contents of file1. The problem with NR == FNR is that code associated with it executes on the contents of file1 when file2 is empty

    – iruvar
    14 hours ago





    sorry I should have said in this particular case file2 and not file1 is empty. Sane behaviour when file2 is empty is to report the contents of file1. The problem with NR == FNR is that code associated with it executes on the contents of file1 when file2 is empty

    – iruvar
    14 hours ago




    1




    1





    @iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.

    – terdon
    14 hours ago







    @iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.

    – terdon
    14 hours ago















    13














    No need for awk, assuming the files are sorted, you can use coreutils join:



    join -o '2.2 1.2 1.3 1.4 1.5' file1 file2


    Output:



    GCF_000014165.1_ASM1416v1_protein.faa     WP_011558474.1  1155234 1156286 44173
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
    GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
    GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
    GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
    GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


    If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:



    join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)





    share|improve this answer






























      13














      No need for awk, assuming the files are sorted, you can use coreutils join:



      join -o '2.2 1.2 1.3 1.4 1.5' file1 file2


      Output:



      GCF_000014165.1_ASM1416v1_protein.faa     WP_011558474.1  1155234 1156286 44173
      GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
      GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
      GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
      GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
      GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
      GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
      GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
      GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


      If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:



      join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)





      share|improve this answer




























        13












        13








        13







        No need for awk, assuming the files are sorted, you can use coreutils join:



        join -o '2.2 1.2 1.3 1.4 1.5' file1 file2


        Output:



        GCF_000014165.1_ASM1416v1_protein.faa     WP_011558474.1  1155234 1156286 44173
        GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
        GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
        GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
        GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
        GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
        GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
        GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
        GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


        If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:



        join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)





        share|improve this answer















        No need for awk, assuming the files are sorted, you can use coreutils join:



        join -o '2.2 1.2 1.3 1.4 1.5' file1 file2


        Output:



        GCF_000014165.1_ASM1416v1_protein.faa     WP_011558474.1  1155234 1156286 44173
        GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
        GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
        GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
        GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
        GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
        GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
        GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
        GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7


        If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:



        join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)






        share|improve this answer














        share|improve this answer



        share|improve this answer








        edited 14 hours ago









        terdon

        133k33268448




        133k33268448










        answered 15 hours ago









        ThorThor

        12.1k13762




        12.1k13762






















            BhushanDhamale is a new contributor. Be nice, and check out our Code of Conduct.










            draft saved

            draft discarded


















            BhushanDhamale is a new contributor. Be nice, and check out our Code of Conduct.













            BhushanDhamale is a new contributor. Be nice, and check out our Code of Conduct.












            BhushanDhamale is a new contributor. Be nice, and check out our Code of Conduct.
















            Thanks for contributing an answer to Unix & Linux Stack Exchange!


            • Please be sure to answer the question. Provide details and share your research!

            But avoid



            • Asking for help, clarification, or responding to other answers.

            • Making statements based on opinion; back them up with references or personal experience.


            To learn more, see our tips on writing great answers.




            draft saved


            draft discarded














            StackExchange.ready(
            function () {
            StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2funix.stackexchange.com%2fquestions%2f510709%2freplacing-matching-entries-in-one-column-of-a-file-by-another-column-from-a-diff%23new-answer', 'question_page');
            }
            );

            Post as a guest















            Required, but never shown





















































            Required, but never shown














            Required, but never shown












            Required, but never shown







            Required, but never shown

































            Required, but never shown














            Required, but never shown












            Required, but never shown







            Required, but never shown







            Popular posts from this blog

            Knooppunt Holsloot

            Altaar (religie)

            Gregoriusmis