Output of command as variable

Question

I'm writing a PBS script to process many files at once and perform multiple actions.

I would like to start by unzipping .gz files (which I later zip) and then process the unzipped file.

The following will unzip the file in $file, but I once I have unzipped the file, I would like the variable $file to refer to the unzipped version:

for file in $READS/*2.fq.gz;
do
    gunzip $file
    # continue script with the gunzipped file  
done

Something like:

for file in $READS/*2.fq.gz;
do
    file=gunzip $file
    # continue script with the gunzipped file  
done

Answer 1

You want to remove the .gz suffix on $file:

file=${file%.gz}

Note that you probably also want to check the result of the gunzip command to see if it failed:

for file in $READS/*2.fq.gz;
do
    if gunzip $file; then
        file=${file%.gz}
        # continue script with the gunzipped file
    else
        # gunzip failed (corrupt file?) and already output an error message
        # try to recover?
    fi
done