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I have a very large file (snippet below). I need to remove any lines where the number in the first column does not increase consecutively from the line above.

For example, I want to keep the first line from my snippet, where the identifier in the first column is "40812." Then I want to preserve the row where "40813" is in the first column (line 3 in my example) and then the row that starts with "40814," and so on. I want to delete any lines that violate this succession, such as the second row.

I have looked here at previous questions/answers for possible solutions and so far have had no success. A solution that has appeared in several questions is:

awk -F',' ' '!seen[$1]++ myFile

I adapted another solution I saw as:

sort -t':' -k 1,1 -u myFile

If anyone could please tell me where I'm going wrong, I would be very grateful. I'm not very experienced with file manipulation.

 40812        20406.000000         0.843859468      1083.209050130      -994.562279080      -993.349611938        22.120868921
 40829        20414.500000         0.891283743      1144.084593627      -994.539001565      -993.349739827        21.177788019
 40813        20406.500000         0.829362077      1064.599666089      -994.546948121      -993.348764740        22.087239027
 40830        20415.000000         0.889606427      1141.931529727      -994.537943593      -993.350242614        21.282490969
 40814        20407.000000         0.822524589      1055.822814442      -994.540118434      -993.348757318        22.083606005
 40831        20415.500000         0.875230513      1123.478077086      -994.523844766      -993.350421831        20.606467962
 40815        20407.500000         0.823511602      1057.089780943      -994.541681744      -993.349315083        22.432111979
 40832        20416.000000         0.846150258      1086.149592126      -994.494220141      -993.349798791        22.309054136
 40816        20408.000000         0.824550451      1058.423286012      -994.543159511      -993.349731194        22.481428146
 40833        20416.500000         0.811604775      1041.805740021      -994.458563132      -993.348626225        21.118428946
 40834        20417.000000         0.787796672      1011.244783236      -994.434062658      -993.347887110        20.963790894
 40817        20408.500000         0.819160081      1051.504008955      -994.537767061      -993.349702160        22.268819809
 40835        20417.500000         0.784857495      1007.471947645      -994.431441227      -993.348167742        20.731789112
 40818        20409.000000         0.807571275      1036.628191427      -994.525675417      -993.349169067        22.332761049
 40836        20418.000000         0.799208319      1025.893192994      -994.446595759      -993.348938468        21.268665075
 40819        20409.500000         0.797104599      1023.192780242      -994.514563564      -993.348491176        22.622548103
 40837        20418.500000         0.819797939      1052.322786256      -994.467698852      -993.349417295        21.013041973
 40820        20410.000000         0.796605925      1022.552664951      -994.513928312      -993.348319789        22.193170071
|improve this question|||||
6

This is exactly the sort of thing that awk excels at:

$ awk '{ if(NR==1 || $1 == last+1){print; last=$1}}' file
 40812        20406.000000         0.843859468      1083.209050130      -994.562279080      -993.349611938        22.120868921
 40813        20406.500000         0.829362077      1064.599666089      -994.546948121      -993.348764740        22.087239027
 40814        20407.000000         0.822524589      1055.822814442      -994.540118434      -993.348757318        22.083606005
 40815        20407.500000         0.823511602      1057.089780943      -994.541681744      -993.349315083        22.432111979
 40816        20408.000000         0.824550451      1058.423286012      -994.543159511      -993.349731194        22.481428146
 40817        20408.500000         0.819160081      1051.504008955      -994.537767061      -993.349702160        22.268819809
 40818        20409.000000         0.807571275      1036.628191427      -994.525675417      -993.349169067        22.332761049
 40819        20409.500000         0.797104599      1023.192780242      -994.514563564      -993.348491176        22.622548103
 40820        20410.000000         0.796605925      1022.552664951      -994.513928312      -993.348319789        22.193170071

Or, a little golfed:

$ awk '(NR==1 || $1 == last+1) && last=$1' file
 40812        20406.000000         0.843859468      1083.209050130      -994.562279080      -993.349611938        22.120868921
 40813        20406.500000         0.829362077      1064.599666089      -994.546948121      -993.348764740        22.087239027
 40814        20407.000000         0.822524589      1055.822814442      -994.540118434      -993.348757318        22.083606005
 40815        20407.500000         0.823511602      1057.089780943      -994.541681744      -993.349315083        22.432111979
 40816        20408.000000         0.824550451      1058.423286012      -994.543159511      -993.349731194        22.481428146
 40817        20408.500000         0.819160081      1051.504008955      -994.537767061      -993.349702160        22.268819809
 40818        20409.000000         0.807571275      1036.628191427      -994.525675417      -993.349169067        22.332761049
 40819        20409.500000         0.797104599      1023.192780242      -994.514563564      -993.348491176        22.622548103
 40820        20410.000000         0.796605925      1022.552664951      -994.513928312      -993.348319789        22.193170071

Explanation

  • if(NR==1 || $1 == last+1) : NR is the current line number. So NR == 1 will only be true while reading the first line of the file. We need this so we will always print the first line. Then, $1 == last +1 will be true if the first field of the line ($1) equals the value stored in the variable last plus 1. Taken together, this means "if this is the last line or if the first field is equal to last + 1", which defines your target lines.
  • print; last=$1 : If either of the two conditions explained above is true, print the line and set the value of last to be the first field of this line so we can process the next.
|improve this answer|||||
  • Thank you very much, terdon, for this detailed explanation. Apologies in advance for what is sure to be a newbie issue... I tried your first solution and nothing seemed to have changed. The second solution (which, if I understand correctly, is just a shortened version of the first?) did lead to the correct screen output. However, the file is unchanged. – user3292696 Nov 28 '19 at 15:12
  • @user3292696 never apologize for being a newbie! None of us were born knowing this stuff! Now, I don't know why the first wouldn't work, they do the same thing with the same logic. But neither will change the original file, they just print the output to the terminal. What you want is to save that output as a new file: awk '(NR==1 || $1 == last+1) && last=$1' file > newfile – terdon♦ Nov 28 '19 at 15:14
  • Well, I know we're not supposed to spam by saying "thank you," but I hope it's OK to make an exception in this case. Thank you for your patience, terdon. Really appreciate it. Awk is very challenging for me. Your fix worked. – user3292696 Nov 28 '19 at 15:30
  • With the magic of Linux, you can use the same awk command to pluck out the alternating series too. You just need to hide the first line of the file, like: tail -n +2 file | Terdon'sAwk. Then it sees 40829 as its first line, and makes a series based on that. – Paul_Pedant Nov 28 '19 at 16:33
  • That's great to know, @Paul_Pedant. I would rather preserve both series. I have this problem because I was sloppy and submitted one simulation twice to the local supercomputer. It is not easy to rerun simulations, so I want to use whatever output I can. – user3292696 Nov 28 '19 at 16:58

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