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Asked: 2026-06-17T09:21:53+00:00

I am new to linux and the command line. I am trying to find

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I am new to linux and the command line. I am trying to find a command to that will allow me to replace white space (in a .csv text file) with a semi-colon for all fields except the first. Please see example below, any help would be gratefully received, I have spent a long time looking for a solution. If you do have an answer could you please explain the command so I can try and learn how and why. Many thanks.

Example of input text:

0   k__Bacteria  p__Firmicutes   c__Bacilli             
1   k__Bacteria  p__Firmicutes   c__Clostridia      
2   k__Bacteria  p__Bacteroidetes    c__Bacteroidia     
3   k__Bacteria  p__Bacteroidetes    c__Bacteroidia

What I need the out put to be:

0   k__Bacteria;p__Firmicutes;c__Bacilli        
1   k__Bacteria;p__Firmicutes;c__Clostridia    
2   k__Bacteria;p__Bacteroidetes;c__Bacteroidia   
3   k__Bacteria;p__Bacteroidetes;c__Bacteroidia
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1 Answer

  1. Editorial Team
    $ cat file
0   k__Bacteria  p__Firmicutes   c__Bacilli     foo     bar
1   k__Bacteria  p__Firmicutes   c__Clostridia  the   quick     brown
2   k__Bacteria  p__Bacteroidetes    c__Bacteroidia     fox jumped      over
3   k__Bacteria  p__Bacteroidetes    c__Bacteroidia     the lazy dogs back

$ awk -v skip=1 '{match($0,"([^[:space:]]+[[:space:]]+){"skip"}"); head=substr($0,1,RSTART+RLENGTH); tail=substr($0,RSTART+RLENGTH+1); gsub(/[[:space:]]+/,";",tail); print head tail}' file
0   k__Bacteria;p__Firmicutes;c__Bacilli;foo;bar
1   k__Bacteria;p__Firmicutes;c__Clostridia;the;quick;brown
2   k__Bacteria;p__Bacteroidetes;c__Bacteroidia;fox;jumped;over
3   k__Bacteria;p__Bacteroidetes;c__Bacteroidia;the;lazy;dogs;back

$ awk -v skip=2 '{match($0,"([^[:space:]]+[[:space:]]+){"skip"}"); head=substr($0,1,RSTART+RLENGTH); tail=substr($0,RSTART+RLENGTH+1); gsub(/[[:space:]]+/,";",tail); print head tail}' file
0   k__Bacteria  p__Firmicutes;c__Bacilli;foo;bar
1   k__Bacteria  p__Firmicutes;c__Clostridia;the;quick;brown
2   k__Bacteria  p__Bacteroidetes;c__Bacteroidia;fox;jumped;over
3   k__Bacteria  p__Bacteroidetes;c__Bacteroidia;the;lazy;dogs;back

$ awk -v skip=3 '{match($0,"([^[:space:]]+[[:space:]]+){"skip"}"); head=substr($0,1,RSTART+RLENGTH); tail=substr($0,RSTART+RLENGTH+1); gsub(/[[:space:]]+/,";",tail); print head tail}' file
0   k__Bacteria  p__Firmicutes   c__Bacilli;foo;bar
1   k__Bacteria  p__Firmicutes   c__Clostridia;the;quick;brown
2   k__Bacteria  p__Bacteroidetes    c__Bacteroidia;fox;jumped;over
3   k__Bacteria  p__Bacteroidetes    c__Bacteroidia;the;lazy;dogs;back
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