Count characters in line after first grep result, but removing new line from count

Question

The problem:

I have multiple text files (.fas), which look like this:

file1.fas:

>species1
AICGICVIAGIAIYIAAICG
>species2
AICGIVVYICAGAYICAGCG

file2.fas:

>species1
AIG
>species2
GCI

I'm interested in counting the number of characters in the second line (it's the same across all the species in one file as they are aligned.

My current one liner:

for i in *.fas; do echo -n "$i," && grep -m 1 -A 1 '>' $i | tail -n 1 | wc -c; done;

This works to an extent but is counting one number higher than the actual number of characters, as it is counting the newline character. How do I fix this so it only counts the number of characters excluding newline characters?

Current output:

file1.fas,21
file2.fas,4

Desired output:

file1.fas,20
file2.fas,3

Answer 1

• | wc -l prints the number of lines.
• | wc -c prints the number of chars, including newline.
• | wc -lc prints both (number of lines first).

So you can simply subtract them: (write it instead of |wc -c)

| wc -lc | awk '{print $2 - $1}'

If you only print your sequence on one line, you can substract 1 instead of the number of newlines.

Or you can use awk only, match the whole line and count its chars:

| awk '{match("[A-Z]*");print RLENGTH}'

RLENGTH is the length of the match (here, it's the whole line). Here, I assume you use only capital letters, else, use . instead of [A-Z].

On vim (text editor, so it could be incompatible with your script), visually select your area (one line or more) and run:

:'<,'>s/[A-Z]*//gn

You can also delete the newline characters with tr (also works for several lines) :

| tr -d '\n' | wc -c

Btw, there is probably lots of other ways to do it.

Answer 2

Use find to find the .fas files and find command will push them onto awk's comnand line, as much as awk can take at a stretch. So the number of awk invocations is minimized.

$ find . -maxdepth 1 -type f -name '*.fas' -exec \
awk -v OFS=, 'FNR==2{print FILENAME, length();nextfile}' {} +

Output:

./file1.fas,20
./file2.fas,3

Answer 3

Use the following perl one-liner, which prints the file name and the length of the second line, comma-delimited. The newlines are stripped using -l flag:

for i in *.fas; do perl -lne 'if ( $. == 2) { print join ",", $ARGV, length $_; last LINE; }' $i ; done

Input:

cat > file1.fas <<EOF
>species1
AICGICVIAGIAIYIAAICG
>species2
AICGIVVYICAGAYICAGCG
EOF

cat > file2.fas <<EOF
>species1
AIG
>species2
GCI
EOF

Output:

file1.fas,20
file2.fas,3

The perl one-liner uses these command line flags:
-e : tells Perl to look for code in-line, instead of in a file.
-n : loop over the input one line at a time, assigning it to $_ by default.
-l : strip the input line separator ("\n" on *NIX by default) before executing the code in-line, and append it when printing.

$ARGV is the name of the current input file.
length $_ is the length of the current line, which has been selected as input line number 2 ($. == 2).
last LINE makes the code skip to the last input line after printing the line length, for speed.

SEE ALSO:

perlrun: command line switches