[SOLVED] sorted in order of decreasing frequency

Issue

I want to be able to show the output in sorted in order of decreasing frequency. If two or more codons have the same frequency, the script should break the tie using the alphabetical order of the codons. In this example, cag and gtt each occur just once, but because c precedes g, cag comes before gtt above.

when I run my script

cat test
aacgtttgtaaccagaactgt
./histogram test
3 aac 
1 gtt 
2 tgt 
1 cag 

but instead, I want to be able to do

./histogram test
3 aac

2 tgt

1 cag

1 gtt

Here what I did

declare -a codons=(aac gtt tgt cag)

for items in  ${codons[@]}
do

        count=$( grep -o $items $1  | sort  -k1,1nr -k2,2 | wc -l)

     # count=$( grep -o $items $1 | uniq -c | wc -l | sort  -k1,1nr -k2,2  )
        echo "$count $items "
done

Solution

Just sort the output.

./histogram test | sort -k1,1nr -k2,2

If you want to include the sort into your script you can append it after the done of your loop:

...
done | sort -k1,1nr -k2,2

By the way: sort | wc -l is wasted time, since sort does not change the number of lines. Just use wc -l.

For your example output of ./histogram test this should print

3 aac
2 tgt
1 cag
1 gtt

Answered By - Socowi

Answer Checked By - Mary Flores (WPSolving Volunteer)