CODEWITHSUNDEEP
linuxgrep
Mark
Mark

Reputation: 323

Use a text file (containing file names) to copy files from current directory to new directory

I have created a file (search.txt) containing file names of .fasta files I want to copy from the current directory (which also contains many unwanted .fasta files). Is it possible to use this text file to find and copy the matching files in the current directory to a new location?

The search.txt file contains a list of names like this:

name_1
name_2
name_3

I tried to build the search term using find and grep, like this:

find . *.fasta | grep -f search.txt

which is returning output like this for each matching file:

./name_1.fasta
./name_2.fasta
./name_3.fasta
name_1.fasta
name_2.fasta
name_3.fasta

It's finding the correct files, but I'm not sure if this output is useful / can be used to copy these files?

Upvotes: 0

Views: 1578

Answers (2)

Benjamin W.
Benjamin W.

Reputation: 52152

Using Bash, you can read all the files from the list into an array:

$ mapfile -t files < search.txt
$ declare -p files
declare -a files=([0]="name_1" [1]="name_2" [2]="name_3")

Then, you can append the desired file extension to all array elements:

$ files=("${files[@]/%/.fasta}")
$ declare -p files
declare -a files=([0]="name_1.fasta" [1]="name_2.fasta" [2]="name_3.fasta")

And finally, move them to the desired location:

$ mv "${files[@]}" path/to/new/location

You don't actually need the intermediate step:

mapfile -t files < search.txt
mv "${files[@]/%/.fasta}" path/to/new/location

Upvotes: 1

644
644

Reputation: 639

To get only matching filenames from search.txt I would do this:

find . -type f -name '*.fasta' -print0 | grep -zf search.txt | xargs -r0 cp -t target-dir/

It will find all files with the extension .fasta, display only the ones with matching patterns in search.txt, and bulk cp them to target-dir, and each filename is terminated with a nullbyte in case filenames contain newlines.

Upvotes: 4

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