Ubuntu – How to copy files with common names and paste them into another folder

To glob for the different names, you can use a for loop like so

for f in /Users/Marine/Descktop/folderGN/{*[Pp]rotein*,*MSMS*,*PSms*}; do echo mv -v -- "$f" /Users/Marine/Descktop/myfolder ; done

Remove the echo after testing to actually move the files.

I have copied your paths exactly (including the possible typo in Descktop?), but you could instead do this with relative paths:

cd /Users/Marine/Descktop/folderGN
for f in *[Pp]rotein* *MSMS* *PSms* ; do echo mv -v -- "$f" ../myfolder ; done 

(remove echo after testing as before)

Shell script and its usage

This can be done with a simple shell script which makes use of find ...|while read var ; do ... done structure ( very common in dealing with filenames ). The bash script below operates on current (top-most) directory and takes single argument for destination.

#!/bin/bash
find -name "genome.txt" -print0 | while IFS= read -r -d '' path
do
    base=$(basename --suffix=".txt"  "$path")
    new_path="${1%/}"/"$base"$counter".txt"
    echo "$path" "$new_path"
    counter=$(( $counter +1 ))
done

>>>NOTE<<<: script uses echo just for testing purposes. When you are satisfied with resulting paths, replace echo with mv to move all filenames or cp to copy all filenames.

Example:

bash-4.3$ tree
.
├── destination
├── dir1
│   └── genome.txt
├── dir2
│   └── genome.txt
├── dir3
│   └── genome.txt
└── move_enumerated.sh

4 directories, 4 files
bash-4.3$ ./move_enumerated.sh  ./destination
./dir2/genome.txt ./destination/genome.txt
./dir3/genome.txt ./destination/genome1.txt
./dir1/genome.txt ./destination/genome2.txt

Improving the script for more flexibility

This script can be further improved to make it more general, where user can specify filename , top directory to traverse, and destination all as command-line arguments:

#!/bin/bash
find "$2"  -name "$1" -print0 | while IFS= read -r -d '' path
do
    base=$(basename --suffix=".txt"  "$path")
    new_path="${3%/}"/"$base"$counter".txt"
    echo "$path" "$new_path"
    counter=$(( $counter +1 ))
done

Test run:

bash-4.3$ ./move_enumerated.sh "genome.txt"  "./testdir" "./testdir/destination"
./testdir/dir2/genome.txt ./testdir/destination/genome.txt
./testdir/dir3/genome.txt ./testdir/destination/genome1.txt
./testdir/dir1/genome.txt ./testdir/destination/genome2.txt

Syntax and theory of operation

Over all the script makes use of command | while read variable ; do ... done structure. This is a very common approach, and it is frequently used to avoid dealing with ls and difficult filenames that can break scripts.

On the left side of the pipe we have find command, which takes directory as argument ( and if that's not given, GNU find which is used in Linux assumes . - the current working directory ). The other options include -name which is the specific filename that we are searching, and -print0 which is used to output results as delimited via non-printable \0 character. It is frequently used to avoid splitting on newline or other characters, because those characters can potentially appear within the filename itself and as a result break the script.

On the right side of the pipe we have while IFS= read -r -d '' ; do . . . done structure. The while loop with read shell built-in is frequently used to real stdin input, which in this case comes from the pipe. IFS= -r and -d '' are necessary to ensure that we receive filenames safely and recognize that each item is delimited with \0.

The rest of the script is fairly easy. We extract basename of the file using basename command. Since in this case we're dealing specifically with known extension and expect to have single dot in the filename, we can use --suffix=".txt" to strip that part out , leaving genome part. We then build new path to file via joining destination , basename, and counter variable. Notice that we use parameter expansion with "${3%/}" argument (destination folder) in our improved script. This is done to ensure that regardless of whether or not user added / character at the command-line ( ./destination or ./destination/ ), we extract only bare directory name, and join it via different / with basename. Notice also that counter variable is not set initially, so the first filename that we receive, will be plain genome.txt After than, counter variable will be incremented and thus created and will show up when we deal with other filenames.

For more info , please read Filenames and Pathnames in Shell: How to do it Correctly.