Need to decompress files and pass the result to a bash script

Paulo Sergio Schlogl

11/17/23, 11:07 AM

I need to use a program that is unable to read compressed files. So I write a script to decompress and then pass the decompressed file to the program.

My script:

#! usr/bin/env bash

dir_in="dir1/$1/$2/$3"
dir_out="Rmes/$1/$2"
mkdir -p ${dir_out}

for file in $(ls -1 ${dir_in})
do
  f=$(gzip -k -c ${dir_in}/${file})
  echo "$f"
  name=${file%.*}
  echo "Calculating the compomd poisson and gaussian data from ${name} file"
  rmes --compoundpoisson -l $4 --max --dna -s ${f} -o "${dir_out}/${name}_k$4_comp_pois"
  #rems --gauss -l $4 --max --dna -s ${dir_out}/${f} -o "${dir_out}/_k$4_gauss"
done

It seems that the script is not working:

PARSE ERROR: Argument: Rmes/$1/$2/outpfilename
             Couldn't find match for argument

gzip: dir1/dir2/dir3/dir4/filename.gz already has .gz suffix -- unchanged

Any of the friends has any suggestion? I really appreciate any tip or script modification.

Paulo

0 + 1

command-line

bash

scripts

steeldriver

11/17/23, 1:11 PM

You should run your script through [www.shellcheck.net](https://www.shellcheck.net/) and fix the bad practices (like unquoted variable expansions / looping over ls output). But probably the main error is that your gzip command is missing the `-d` / `--decompress` option.

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