How can I count number of a specific character in a column for each line and add as new column using AWK?

Question

I would like to count the number of N characters in the second column of a file and then print this count to the third column. Example input file (tab-separated):

sample1 TCTNG
sample2 CCNGGGGGTN
sample3 GGGNNNTC

Desired output (tab-separated):

sample1 TCTNG   1
sample2 CCNGGGGGTN  2
sample3 GGGNNNTC    3

I can get a messy version doing the following, but I would like a one-liner, preferably in awk.

> awk -F '\t' '{print $2}' file.txt | awk -FN '{print NF-1}' > NCount.txt
> paste -d '\t' file.txt NCount.txt

sample1 TCTNG   
    1
sample2 CCNGGGGGTN  
    2
sample3 GGGNNNTC
    3

Answer 1

awk 'BEGIN{FS=OFS="\t"} {print $0, gsub(/N/,"",$2)}' file
sample1 TCTNG   1
sample2 CCNGGGGGTN  2
sample3 GGGNNNTC    3

Based on : How to print the count of pattern at each line?

Answer 2

The gsub() function returns the number of made substitutions. You may use this fact to count the number of N characters in the 2nd field and to add this number as a new field on each line:

$ awk -F '\t' '{ $3 = gsub("N","N",$2) }; 1' file
sample1 TCTNG 1
sample2 CCNGGGGGTN 2
sample3 GGGNNNTC 3

The output is caused by the trailing 1 (it is equivalent to using { print } or { print $0 }).

Set the value of the special variable OFS to use another field delimiter than the default (space) in the output. Here I'm using whatever the input field delimiter is set to:

$ awk -F '\t' 'BEGIN { OFS=FS } { $3 = gsub("N","N",$2) }; 1' file
sample1 TCTNG   1
sample2 CCNGGGGGTN      2
sample3 GGGNNNTC        3

---

Simirlarly in Perl, but using the tr operator in place of gsub():

$ perl -MEnglish -a -F '\t' -e 'BEGIN { $OFS="\t"; $ORS="\n" } print @F, ($F[1] =~ tr/N/N/)' file
sample1 TCTNG   1
sample2 CCNGGGGGTN      2
sample3 GGGNNNTC        3

Answer 3

Using Raku (formerly known as Perl_6)

raku -ne 'put ~$/.join("").chars if m:g/N*/;'  

Sample Input:

sample0 TCTG
sample1 TCTNG
sample2 CCNGGGGGTN
sample3 GGGNNNTC

Sample Output:

sample0 TCTG    0
sample1 TCTNG   1
sample2 CCNGGGGGTN  2
sample3 GGGNNNTC    3

Above code: print the Raku $_ topic variable first (followed by a \t), then print a count of the the join("") -concatenated N matches, and add as a new column to the end of each line.

https://raku.org