Now following on from renaming the files of interest (fna.gz) I now need to loop through folder1.
As I loop through folder1 I am trying to first of all capture the first word in the file before the first underscore, for example if the folder name is /Long_John_Silver/ then I am trying to capture only "Long".
Then I want to check whether there is a folder with the same name "Long" in a distant directory /another/directory/ and if there is then a move onto the next folder in folder1, but if there isn't then I create a new folder with the captured name i.e. "Long".
Here's my work so far, I am struggling with the capturing of "Long" part.
Code:
for fldr in /folder1/folder2/.fna.gz ; do
## Trying to regex capture here but I'm unclear on the syntax, there's expansion, grep etc but don't know which to use.
new_fldr = ${fldr}
## Then the test for existence.
if [-f /another/directory/$new_fldr ]; then
echo "Folder exists already, moving on..." ;
else [ ! -f /another/directory/$new_fldr ];
echo "Folder not present, creating folder..." ;
cd /another/directory/ ;
mkdir $new_fldr ;
for fldr in ./folder1/* ; do
basenm=${fldr##*/}
if [[ "$basenm" = *_* ]] && [ -d "$fldr" ]; then
new_fldr=${basenm%%_*}
if [ -d "/another/directory/$new_fldr" ]; then
echo "Folder exists already, moving on..." ;
else
echo "Folder not present, creating folder..." ;
mkdir "/another/directory/$new_fldr" ;
fi
else
echo "not looking at $fldr"
fi
done
Notice how most references to basenm, fldr and newdir are quoted, this is necessary if any of your folder names could ever contain white space characters (like space or newline).
There is no need to cd into /another/directory to create folders, and doing this will cause the next loop to fail, so just pass the full directory path to mkdir and keep the current directory where it is.
This User Gave Thanks to Chubler_XL For This Post:
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