Error in bash script: arithmetic error - bash

Question

I am wrote a simple script to extract text from a bunch of files (*.out) and add two lines at the beginning and a line at the end. Then I add the extracted text with another file to create a new file. The script is here.
#!/usr/bin/env bash
#A simple bash script to extract text from *.out and create another file
for f in *.out; do
#In the following line, n is a number which is extracted from the file name
n=$(echo $f | cut -d_ -f6)
t=$((2 * $n ))
#To extract the necessary text/data
grep " B " $f | tail -${t} | awk 'BEGIN {OFS=" ";} {print $1, $4, $5, $6}' | rev | column -t | rev > xyz.xyz
#To add some text as the first, second and last lines.
sed -i '1i -1 2' xyz.xyz
sed -i '1i $molecule' xyz.xyz
echo '$end' >> xyz.xyz
#To combine the extracted info with another file (ea_input.in)
cat xyz.xyz ./input_ea.in > "${f/abc.out/pqr.in}"
done
./script.sh: line 4: (ls file*.out | cut -d_ -f6: syntax error: invalid arithmetic operator (error token is ".out) | cut -d_ -f6")
How I can correct this error?

Answer 1

In bash, when you use:
$(( ... ))
it treats the contents of the brackets as an arithmetic expression, returning the result of the calculation, and when you use:
$( ... )
it executed the contents of the brackets and returns the output.
So, to fix your issue, it should be as simple as to replace line 4 with:
n=$(ls $f | cut -d_ -f6)
This replaces the outer double brackets with single, and removes the additional brackets around ls $f which should be unnecessary.

Answer 2

The arithmetic error can be avoided by adding spaces between parentheses. You are already using var=$((arithmetic expression)) correctly elsewhere in your script, so it should be easy to see why $( ((ls "$f") | cut -d_ -f6)) needs a space. But the subshells are completely superfluous too; you want $(ls "$f" | cut -d_ -f6). Except ls isn't doing anything useful here, either; use $(echo "$f" | cut -d_ -f6). Except the shell can easily, albeit somewhat clumsily, extract a substring with parameter substitution; "${f#*_*_*_*_*_}". Except if you're using Awk in your script anyway, it makes more sense to do this - and much more - in Awk as well.
Here is an at empt at refactoring most of the processing into Awk.
for f in *.out; do
awk 'BEGIN {OFS=" " }
# Extract 6th _-separated field from input filename
FNR==1 { split(FILENAME, f, "_"); t=2*f[6] }
# If input matches regex, add to array b
/ B / { b[++i] = $1 OFS $4 OFS $5 OFS $6 }
# If array size reaches t, start overwriting old values
i==t { i=0; m=t }
END {
# Print two prefix lines
print "$molecule"; print -1, 2;
# Handle array smaller than t
if (!m) m=i
# Print starting from oldest values (index i + 1)
for(j=1; j<=m; j++) {
# Wrap to beginning of array at end
if(i+j > t) i-=t
print b[i+j]; }
print "$end" }' "$f" |
rev | column -t | rev |
cat - ./input_ea.in > "${f/foo.out/bar.in}"
done
Notice also how we avoid using a temporary file (this would certainly have been avoidable without the Awk refactoring, too) and how we take care to quote all filename variables in double quotes.
The array b contains (up to) the latest t values from matching lines; we collect these into an array which is constrained to never contain more than t values by wrapping the index i back to the beginning of the array when we reach index t. This "circular array" avoids keeping too many values in memory, which would make the script slow if the input file contains many matches.