Renaming files with the same names as directory - bash script - linux

Question

I want to rename my files so that they are name with the same name as the folder.
I have a main folder that has around 1000 folders. each of these folders have another file within it. in that very last folder, I have files with different extentions. and I want to rename the files that have pdb extention.
here's the strcuture of my folders :
pv----|
|--m10\ pk\ result0.pdb result1.pdb result2.pdb
|--m20\ pk\ result0.pdb result1.pdb result2.pdb
|--m30\ pk\ result0.pdb result1.pdb result2.pdb
I want something like this :
pv----|
|--m10\ pk\ m10_result0.pdb m10_result1.pdb m10_result2.pdb
|--m20\ pk\ m20_result0.pdb m20_result1.pdb m20_result2.pdb
|--m30\ pk\ m30_result0.pdb m30_result1.pdb m30_result2.pdb
that's the code I made but It's not working ..
for d in MD_PR2 / * / * /
do
(cd "$d" && for file in *.pdb ; do mv "$file" "${file/result/$d_result}" ; done)
done
my code is deleting "result" of each file's name and I don't know. it becomes 0.pdb , 1.pdb ..etc
thank you very much

Answer 1

Before:
user#pc:~$ tree
.
├── m10
│   └── pk
│   ├── result0.pdb
│   ├── result1.pdb
│   └── result2.pdb
├── m20
│   └── pk
│   ├── result0.pdb
│   ├── result1.pdb
│   └── result2.pdb
└── m30
└── pk
├── result0.pdb
├── result1.pdb
└── result2.pdb
Your code is not working because $d_result is being interpreted as a variable name, not as a concatenation of $d and _result. I suggest using ${d}_result.
However I would suggest another approach, one that doesn't need to cd into each directory.
Code:
shopt -s globstar
for file in **; do
if [[ "$file" =~ ".pdb" ]] ; then
mv "$file" `echo $file | sed -e 's/\(.*\)\/\(.*\)\/\(.*.pdb\)/\1\/\2\/\1_\2_\3/'`;
fi;
done;
After:
user#pc:~$ tree
.
├── m10
│   └── pk
│   ├── m10_pk_result0.pdb
│   ├── m10_pk_result1.pdb
│   └── m10_pk_result2.pdb
├── m20
│   └── pk
│   ├── m20_pk_result0.pdb
│   ├── m20_pk_result1.pdb
│   └── m20_pk_result2.pdb
└── m30
└── pk
├── m30_pk_result0.pdb
├── m30_pk_result1.pdb
└── m30_pk_result2.pdb
Code explanation:
shopt -s globstar: Allow for ** to be expanded into "all files and directories recursively"
Variable "file" contains filenames including directories
Check "file" against "$file" =~ ".pdb" to ignore working with directories
Generate newfilename with sed:
Search and replace: s/search/replace/
Find something like dir1/dir2/smthg.pdb: (.*)/(.*)/(.*.pdb)
Replace with dir1/dir2/dir1_dir2_smthg.pdb: \1/\2/\1_\2_\3 (replace with \1_\2_\3 if you also want to move renamed files into parent dir)
(I removed some backslashes for readability)
mv file to newfilename