I have two directories with files that end in two different extensions:

Folder A (1348 FILES)

file.profile
file1.profile
file2.profile
file3.profile #<-- odd one out

Folder B (1204 FILES)

file.dssp
file1.dssp
file2.dssp

I have some files in folder A that are not found in folder B and should be removed for example file3.profile would be deleted as it is not found in folder B. I just want to retain those that are common in their filename, but excluding extension to end up with 1204 files in both I saw some bash lines using diff but it does not consider this case, where the ones I want to remove are those that are not found in the corresponding other file.

CodePudding user response：

Here is a way to do it:

• for both A and B directories, list the files under each directory, without the extension.
• compare both lists, show only the file that does not appear in both.

Code:

#!/bin/bash

>a.list
>b.list

for file in A/*
do
    basename "${file%.*}" >>a.list
done

for file in B/*
do
    basename "${file%.*}" >>b.list
done

comm -23 a.list b.list

# cleanup
rm -f a.list b.list

• "${file%.*}" removes the extension
• basename removes the path
• comm -23 ... shows only the lines that appear only in a.list

CodePudding user response：

With find:

find 'folder A' -type f -name '*.fasta.profile' -exec sh -c \
'! [ -f "folder B/$(basename -s .fasta.profile "$1").dssp" ]' _ {} \; -print

Replace -print by -delete when you will be convinced that it does what you want.

Or, maybe a bit faster:

find 'folder A' -type f -name '*.fasta.profile' -exec sh -c \
'for f in "$@"; do [ -f "folder B/$(basename -s .fasta.profile "$f").dssp" ] || echo rm "$f"; done' _ {}  

Remove echo when you will be convinced that it does what you want.

CodePudding user response：

Try this Shellcheck-clean Bash program:

#! /bin/bash -p

folder_a=PATH_TO_FOLDER_A
folder_b=PATH_TO_FOLDER_B

shopt -s nullglob
for ppath in "$folder_a"/*.profile; do
    pfile=${ppath##*/}
    dfile=${pfile%.profile}.dssp
    dpath=$folder_b/$dfile
    [[ -f $dpath ]] || echo rm -v -- "$ppath"
done

• It currently just prints what it would do. Remove the echo once you are sure that it will do what you want.
• shopt -s nullglob makes globs expand to nothing when nothing matches (otherwise they expand to the glob pattern itself, which is almost never useful in programs).
• See Removing part of a string (BashFAQ/100 (How do I do string manipulation in bash?)) for information about the string manipulation mechanisms used (e.g. ${ppath##*/}).