Hey everyone!

I have a tab delimited data set which I want to create an output contained the calculation of number of those lines with a certain value in 2nd and 3rd column.

my input file is like this:

ID1   1   10M   AAATTTCCGG
ID2   5    4M    ACGT
ID3   5    8M    ACCTTGGA
ID4   5    8M    ACCTTGGA
ID5   5    8M    ACCTTGGA
ID6   20   3M   TCG
ID7   20   3M   TCG
ID8   20   12M   AACCTTGGCCTT
ID9   20   12M   AACCTTGGCCTT
ID10   20   12M   AACCTTGGCCTT

1    10M    1    AAATTTCCGG
5    4M     1    ACGT
5    8M     3    ACCTTGGA
20   3M    2    TCG
20   12M   3   AACCTTGGCCTT

Try the below,

cut -f2- FileName | sort | uniq -c

Let us know if the order matters (or just add | sort -nk1 -k2 after the script).

awk 'END {
  for (k in c) 
    print k, c[k], d[k] 
  }
{
  k = $2 OFS $3
  c[k]++; d[k] = $NF
  }' infile

Thanks Athix. I tried this code. But it didn't work. It just gives value 1 for all lines in the first column which is not true. And it keeps repeating the lines with the same values in 2nd and 3rd and 4th columns which I don't want.

---------- Post updated at 03:49 PM ---------- Previous update was at 03:46 PM ----------

Thnaks radoulov. I'm really newbie! I need more explanation. I tried to copy and paste what you said into terminal but I couldn't manage to give the path for the input file. Let me why although I know it is stupid! BTW, I already sorted my file using this script:

sort -n -k1 -k2 <filename>

awk 'END {  
   for (k in c)      
    print k, c[k], d[k]    
    } 
{   
  k = $2 OFS $3  
  c[k]++; d[k] = $NF   
    }' <filename>

$ awk '{print $3,$2,$4}' input.txt | sort | uniq -c | awk '{print $3,$2,$1,$4}' | sort -n
1 10M 1 AAATTTCCGG
5 4M 1 ACGT
5 8M 3 ACCTTGGA
20 12M 3 AACCTTGGCCTT
20 3M 2 TCG

Thanks radoulov! It works perfectly! It just prints the last column of my dataset as the last column of output. In my real data I want the 10th column for the last column in the output! Thanks alot!