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Asked: 2026-06-07T17:00:45+00:00

Basically, I need a script that can solve the problem in very short time.

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Basically, I need a script that can solve the problem in very short time. I have two files:

$ head -n 6 fcu.tsv

NM576455     0.324009324     0.578896174     2577
NM539570     0.204545455     0.607877092     2247
NM337132     0.288973384     0.673636364     792
NM374379     0.308300395     0.42            762
NM373443     0.263043478     0.547132867     1383
NM371839     0.298210736     0.492857143     1512

$ head -n 6 mart.tsv

NM539570 ILMN_2199362    15      58.52   protein_coding
NM576455 ILMN_2195138    1       65.74   protein_coding  nucleus cellular_component      SAM_2
NM576455 ILMN_2195138    1       65.74   protein_coding  protein binding molecular_function      SAM_2
NM576455 ILMN_1709067    1       65.74   protein_coding  nucleus cellular_component      SAM_2
NM576455 ILMN_1709067    1       65.74   protein_coding  protein binding molecular_function      SAM_2
NM576455 ILMN_2195138    1       65.74   protein_coding  nucleus cellular_component      SAM_type1

We need to append the 2nd, 3rd, and 4th fields of fcu.tsv to mart.tsv for each NM id in very short time.

$ head out.tsv

NM539570 ILMN_2199362    15      58.52   protein_coding  0.204545455     0.607877092     2247
NM576455 ILMN_2195138    1       65.74   protein_coding  nucleus cellular_component      SAM_2 0.324009324   0.578896174     2577
    NM576455 ILMN_2195138    1       65.74   protein_coding  protein binding molecular_function      SAM_2 0.324009324   0.578896174     2577
    NM576455 ILMN_1709067    1       65.74   protein_coding  nucleus cellular_component      SAM_2 0.324009324   0.578896174     2577
    NM576455 ILMN_1709067    1       65.74   protein_coding  protein binding molecular_function      SAM_2 0.324009324   0.578896174     2577
    NM576455 ILMN_2195138    1       65.74   protein_coding  nucleus cellular_component      SAM_type1 0.324009324   0.578896174     2577

This is what I did in matlab (I prefer that solution fix the bad codes here to make it faster rather than writing a new one)

fr1 = fopen('fcu.tsv', 'r');
fr2 = fopen('mart.tsv', 'r');

fw = fopen('out.tsv', 'w');

while feof(fr1) == 0
   line = fgetl(fr1);
   scan = textscan(line, '%s%f%f%d');

   frewind(fr2);

    while feof(fr2) == 0
        line2 = fgetl(fr2);
        scan2 = textscan(line2, '%s%s%s%f%s%s%s%s');

            if scan{1}{1} == scan2{1}{1} 

                fprintf(fw, '%s\t%f\t%f\t%d\n', line2, scan{2}, scan{3}, scan{4});

            end

    end

end

Help is appreciated

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1 Answer

  1. Editorial Team

    This is a command-line centric solution, works on any system supporting coreutils, apologies if it is not applicable in your case.

    If mart.tsv was padded properly, as in:

    NM539570 ILMN_2199362    15      58.52   protein_coding  NA      NA                 NA                      NA
NM576455 ILMN_2195138    1       65.74   protein_coding  nucleus cellular_component NA                      SAM_2
NM576455 ILMN_2195138    1       65.74   protein_coding  protein binding            molecular_function      SAM_2
NM576455 ILMN_1709067    1       65.74   protein_coding  nucleus cellular_component NA                      SAM_2
NM576455 ILMN_1709067    1       65.74   protein_coding  protein binding            molecular_function      SAM_2
NM576455 ILMN_2195138    1       65.74   protein_coding  nucleus cellular_component NA                      SAM_type1

    The solution could be a simple join (see info join): 

    $ join <(sort mart.tsv) <(sort fcu.tsv) | column -t
NM539570  ILMN_2199362  15  58.52  protein_coding  NA       NA                  NA                  NA         0.204545455  0.607877092  2247
NM576455  ILMN_1709067  1   65.74  protein_coding  nucleus  cellular_component  NA                  SAM_2      0.324009324  0.578896174  2577
NM576455  ILMN_1709067  1   65.74  protein_coding  protein  binding             molecular_function  SAM_2      0.324009324  0.578896174  2577
NM576455  ILMN_2195138  1   65.74  protein_coding  nucleus  cellular_component  NA                  SAM_2      0.324009324  0.578896174  2577
NM576455  ILMN_2195138  1   65.74  protein_coding  nucleus  cellular_component  NA                  SAM_type1  0.324009324  0.578896174  2577
NM576455  ILMN_2195138  1   65.74  protein_coding  protein  binding             molecular_function  SAM_2      0.324009324  0.578896174  2577

    column comes from the bsdmainutils package.

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