Provisos and assumptions:
- OP mentions needing to process multiple files; for this answer I'm going to focus on a single file; OP can start another question if issues arise with a multi-file solution
- OP mentions wanting to
replace some strings but it's not clear (to me) if the original file is to be overwritten or a new file is to be created; for this answer I'm going to focus on generating the 'modified' output; OP can expand on this solution (below) based on final requirements
- examples seem to imply 4x different search patterns (
alpha, beta, betaR_red, epsilon_gamma); I'm going to assume there could be a variable number of patterns that need to be searched for
- for simplicity sake I'm going to assume the search patterns are stored in an array
- search patterns contain no leading/trailing white space
- search patterns are relatively simple and do not contain any special characters (eg, line feeds)
Sample input file:
$ cat input.txt
pow(alpha,2) + pow(beta,2)
(3*pow(betaR_red,2))
2/pow(gammaBlue,3))
-pow(epsilon_gamma,2)+5
Array of search patterns:
$ var=(alpha beta betaR_red epsilon_gamma 'double helix')
$ typeset -p var
declare -a var=([0]="alpha" [1]="beta" [2]="betaR_red" [3]="epsilon_gamma" [4]="double helix")
The general idea is to use sed to do a multi-pattern search of the file based on the contents of the var[] array. This means we need a way to reference the array in a manner that will be suitable for a sed multi-pattern match (ie, values need to be separated by a pipe (|).
By assigning IFS='|' we can 'reformat' the array contents to work as a multi-pattern search string for sed:
$ echo "${var[*]}"
alpha beta betaR_red epsilon_gamma double helix
$ IFS='|' varX="${var[*]}" ; echo "${varX}"
alpha|beta|betaR_red|epsilon_gamma|double helix
Which brings us to the sed command:
$ IFS='|' sed -E "s/pow\((${var[*]}),2\)/square(\1)/g" input.txt
Where:
sed -E - run with extended regex support
pow\( / ,2\) - search for our pow(..,2) string, escaping the parens so they are not evaluated as delimiters of a regex group
IFS='|' / (${var[*]}) - expand array var using '|' as value delimiter; by wrapping in parens this becomes our first (and only) search group
square( / ) - replacement string for pow( / ,2) pattern
\1 - copy contents of our search group, eg, if we matched on pow(beta,2) then \1 == beta
If we execute the above as set -xv ; IFS='|' sed ...; set +xv we will generate the following 'debug' output showing how the sed command is expanded with the values of the var array:
++ IFS='|'
++ sed -E 's/pow\((alpha|beta|betaR_red|epsilon_gamma|double helix),2\)/square(\1)/g' input.txt
The actual output of the above sed command:
square(alpha) + square(beta) # 2x changes
(3*square(betaR_red)) # 1x change
2/pow(gammaBlue,3)) # no changes
-square(epsilon_gamma)+5 # 1x change