I have a shell command with the following format:
my_cmd -I file1.inp -O file1.out
Where some processing is done on file1.inp and the results are stored in file1.out
In my main directory, I have many files with the format: *.inp and I would like to run this command for all of them and the store the results to *.out. Can I only use shell script to achieve this?
You can use a simple loop:
for file in *.inp ; do
my_cmd -I "${file}" -O "${file%%.inp}.out"
done
${file%%.inp} is a so called parameter expansion. It will effectively remove the extension .inp from the input filename.
One thing (thanks Jean-François Fabre). If the folder does not contain any .inp files the above loop would run once with $file having the literal value *.inp. To avoid that you need to set the nullglob option:
shopt -s nullglob # set the nullglob option
for file in *.inp ; do
my_cmd -I "${file}" -O "${file%%.inp}.out"
done
shopt -u nullglob # unset the nullglob option
$file is a file. 1) it could be a directory, 2) if there are no .inp files in the directory it calls the command with *.inp
nullglob : after shopt -s nullglob, the *.inp will resolve to the empty string, avoiding the loop body from being executed.
& symbol. In your for loop, you could write my_cmd -I "${file}" -O "${file%%.inp}.out" &Using GNU parallel
parallel my_cmd -I {} -O {.}.out ::: *.inp
By default, this will jobs in parallel, one job per core. {} is an unchanged argument, {.} is the same argument minus its extension. The arguments are taken from the words that follow :::.
ls *.inp| xargs -l1 -I % my_cmd -I % -O %.out
ls will modify filenames as soon as they contain problematic letters. find won't do that. Don't parse the results of ls. Period.ls | xargs by a safer find -exec