So the output for the given script is 10. When the script is run it first asks to enter amino acid (in this case ALA) that is taken the value of AAA with which the script works with. AAA can be any of the value as given in the if statement like AAA == ALA, AAA == ARG and any of the written values in the if statement.

Let's take the quote:

Code:

c<B>r<56>a<2643>R<ALA>A<N> 5.654 16.636 -19.419 1.55 el=N oc=1;tf=27.14
c<B>r<56>a<2644>R<ALA>A<CA> 4.306 16.969 -19.795 1.7 el=C oc=1;tf=27.77
c<B>r<56>a<2645>R<ALA>A<C> 4.139 18.435 -20.144 1.7 el=C oc=1;tf=29.41
c<B>r<56>a<2646>R<ALA>A<O> 3.619 18.808 -21.204 1.52 el=O oc=1;tf=30.63
c<B>r<56>a<2647>R<ALA>A<CB> 3.373 16.628 -18.664 1.7 el=C oc=1;tf=28.99
c<B>r<88>a<2887>R<ALA>A<N> -3.023 7.753 -19.907 1.55 el=N oc=1;tf=20.84
c<B>r<88>a<2888>R<ALA>A<CA> -3.018 7.206 -18.575 1.7 el=C oc=1;tf=17.38
c<B>r<88>a<2889>R<ALA>A<C> -1.627 6.647 -18.364 1.7 el=C oc=1;tf=18.59
c<B>r<88>a<2890>R<ALA>A<O> -1.086 5.92 -19.197 1.52 el=O oc=1;tf=14.88
c<B>r<88>a<2891>R<ALA>A<CB> -4.015 6.09 -18.472 1.7 el=C oc=1;tf=18.6

This output ( the one given in quotes above) is made after the command

Code:

 voronota get-balls-from-atoms-file --annotated

and then through pipes are pased to

Code:

 grep -o -i "$AAA" | wc -l | awk '{print $1}'

which in turn gives an output as an integer 10 showing how many times ALA does occur in the dataset (look in quote above).

However I want once the output from

Code:

 voronota get-balls-from-atoms-file --annotated

is passed to pipes

Code:

 grep -o -i "$AAA" | wc -l | awk '{print $1}'

to return me a numerical value of 2.

Why 2? If you look at the quote above the first 5 lines have ALA ( given 5 times in the lines ...r<>a..R<ALA>...) in them but these ALA words are numbered exactly the same (as belonging to 56): (

Code:

c<B>r<56>a<2644>R<ALA>A<CA> 4.306 16.969 -19.795 1.7 el=C oc=1;tf=27.77
c<B>r<56>a<2644>R<ALA>A<CA> 4.306 16.969 -19.795 1.7 el=C oc=1;tf=27.77
c<B>r<56>a<2645>R<ALA>A<C> 4.139 18.435 -20.144 1.7 el=C oc=1;tf=29.41
c<B>r<56>a<2646>R<ALA>A<O> 3.619 18.808 -21.204 1.52 el=O oc=1;tf=30.63
c<B>r<56>a<2647>R<ALA>A<CB> 3.373 16.628 -18.664 1.7 el=C oc=1;tf=28.99

The same reasoning goes for ALA and number 88 (quote below) which also occurs 5 times with ALA. So total occurence of ALA (in the quote above) would be 10 but I want it to be 2 (as occurence of ALA is 1 for each number (56 & 88)). The ALA (or any of the chosen 20 AAA values) is constant in this case while numbers change and can take any integer from 1 to 1000.

Code:

c<B>r<88>a<2887>R<ALA>A<N> -3.023 7.753 -19.907 1.55 el=N oc=1;tf=20.84
c<B>r<88>a<2888>R<ALA>A<CA> -3.018 7.206 -18.575 1.7 el=C oc=1;tf=17.38
c<B>r<88>a<2889>R<ALA>A<C> -1.627 6.647 -18.364 1.7 el=C oc=1;tf=18.59
c<B>r<88>a<2890>R<ALA>A<O> -1.086 5.92 -19.197 1.52 el=O oc=1;tf=14.88
c<B>r<88>a<2891>R<ALA>A<CB> -4.015 6.09 -18.472 1.7 el=C oc=1;tf=18.6

I want the count of AAA to be printed to terminal as 2 (regarding the qoute above which has 56 and 88) and not 10 when the script is run. If the line r<56> is repeated 5 times (as in the quote above regarding 56) it also gives AAA 5 times (in this case ...R<ALA>...), but I want the count for all occurences of ALA at 56 to be 1. All occurences of specific AAA at 88 be given the value 1 as well and so on. Regarding the number 88, 99 or any other it is arbitrary and can change, hence your question about 88, 99 as these are just different numbers as 56.

Hope it is clearer now :-) If not let me know I'll try to rephrase everything.