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I need to figure it out how many times a particular string shows up in column 4.

This is my data:

25 48656721 48656734 FAM132B ENSCAFT00000019683 4 0.51 
X 53969937 53969950 FAM155B ENSCAFT00000026508 5 0.57 
3 42203721 42203906 FAM169B ENSCAFT00000017307 5 0.54 
36 28947780 28947831 FAM171B ENSCAFT00000046981 5 0.51 
10 45080519 45080773 FAM171B ENSCAFT00000003744 9 -0.53 
3 61627122 61627446 FAM193A ENSCAFT00000023571 13 0.64 
3 61626373 61626466 FAM193A ENSCAFT00000023571 6 0.51 
15 55348822 55349196 FAM193A ENSCAFT00000045012 5 0.52 

This is a portion of my data. So, I'd want the output to be:

1 FAM132B
1 FAM155B
1 FAM169B
2 FAM171B
3 FAM193A

And so on - for the rest of my data. What's a command that would work?

One simplistic solution would be to use awk to pull column 4; uniq -c to count them; and another sort to put them in order by the second column (the old column 4 data):

awk 'print $4' < data | uniq -c | sort -k2

On your (updated) sample input, this gives:

 1 FAM132B
 1 FAM155B
 1 FAM169B
 2 FAM171B
 3 FAM193A

Use awk:

awk 'a[$4]++ ENDfor(s in a)print a[s]" "s' file

• 
  a[$4]++ increments the array element whose index has the name of the 4th column. When finishing trough the file, that array contains counters of all occurences of the 4th column.


• 
  END: indicates a block of code that runs when awk is trough the file.
  
  
  • 
    for(s in a) run trough the array...
  
  
  • 
    print a[s]" "s} ... and print its values and indexes.
  
  

The output:

1 FAM169B
3 FAM193A
1 FAM132B
1 FAM155B
2 FAM171B

Assuming the delimiter is a single space:

cut -d' ' -f4 infile | sort | uniq -c

Note that uniq filters adjacent matching lines so you need to sort first e.g. with this input:

FAM193A
FAM155B
FAM169B
FAM171B
FAM132B
FAM193A
FAM132A
FAM132B
FAM155B
FAM169B
FAM171B
FAM171A
FAM193A
FAM132A

using sort | uniq -c produces:

 2 FAM132A
 2 FAM132B
 2 FAM155B
 2 FAM169B
 1 FAM171A
 2 FAM171B
 3 FAM193A

while uniq -c | sort -k2 produces:

 1 FAM132A
 1 FAM132A
 1 FAM132B
 1 FAM132B
 1 FAM155B
 1 FAM155B
 1 FAM169B
 1 FAM169B
 1 FAM171A
 1 FAM171B
 1 FAM171B
 1 FAM193A
 1 FAM193A
 1 FAM193A