awk -v 'OFS=\t' 'NF == 2 { print $1, "none", $2; next } 1' input.txt > output.txt
Adjust depending on the characteristics of your input file. I assume every line with only 2 fields should have a "none" inserted. Otherwise, all other lines are just passed through unchanged (the purpose of the 1 at the end).
sort -k3n,3 filename | tail -5 | cut -d " " -f1,6-7
The above command will sort the file on the 3rd field. Now, I am piping this output to the tail command to print the top 5 numbers in the 3rd column. However, if you need only the first column and this 3rd column in the output, you can pipe the output to cut command.
Testing
cat filename
T_235820.1| 139697 192 0
xm|161622288|ref|RT_340093.1| 153819 2607 0
xm|75755638|ref|RT_557407.1| 153821 1937 0
xm|108773031|ref|RT_678101.1| 161452 1688 0
xm|30352011|ref|RT_784766.1| 150568 105 0
T_235820.1| 139697 192 0
xm|161622288|ref|RT_340093.1| 153819 607 0
xm|75755638|ref|RT_557407.1| 153821 937 0
xm|108773031|ref|RT_678101.1| 161452 1881 0
xm|30352011|ref|RT_784766.1| 150568 1051 0
Now, I run the above command on this file.
sort -k3n,3 filename | tail -5 | cut -d " " -f1,6-7
The output that I get is,
xm|30352011|ref|RT_784766.1| 1051
xm|108773031|ref|RT_678101.1| 1688
xm|108773031|ref|RT_678101.1| 1881
xm|75755638|ref|RT_557407.1| 1937
xm|161622288|ref|RT_340093.1| 2607
EDIT
You can add the -g flag for floating point and negative numbers as well in case if you have any in your file. The command would look like,
sort -k3ng,3 filename | tail -5 | cut -d " " -f1,6-7
Best Answer