Shell Programming and Scripting

I am trying to write a script that loops through all the folders within a given folder.
My intention is to access each folder and rename each file ending with fna.gz with the name of the folder it resides in.

Code:

#!/bin/bash

cd /p/w/d/

for f in /p/w/d/*; do
   echo $f

done

I'm going to take this step by step because first of all at this point if I print "f" it prints the whole pwd including the folders i.e. p/w/d/folder1. Instead of printing just folder1. So firstly how can I get it to print just folder1?

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Code:

find . -name *fna.gz | while read f ; do fl=${f%/*}; fld=${fl##*/} ; echo mv "$f" "$fl/${fld}_${f##*/}" ; done

Test first. To perform rename, update as needed then remove echo

If you remove the full path from the for loop, what does it give you?

Code:

#!/bin/bash
cd /p/w/d/
for f in *; do
   echo $f
done

Code:

for a in `find /p/w/d -type f -name '*.fna.gz'`
{
 d=${a%/*}
 mv $a ${a%.*}.${d##*/}
}

It returns unwanted files and folders.

What were "unwanted folders" in the context of your post#1?

Thanks, your solution works. I'm just trying to decode what you've done.

So I see here that the find function looks for files of a given type i.e. .fna.gz.
And then the pipe ( | ) passes each file to be read.

Code:

 find . -name *fna.gz | while read f ; do

Now as the files are being read something is going on that I can't make out.
You seem to be creating 2 variables, the first of which captures the name of the folder and then the captures the name of the file in that folder. Is this correct?
Is this a regex? What do the values {}, % and # mean?

Code:

fl=${f%/*}; fld=${fl##*/} ;

And then here you rename the files.

Code:

mv "$f" "$fl/${fld}_${f##*/}" ;