Batch rename files

Script name: batchRenameFiles.sh

Script to quickly rename many files. Can replace all (-m full) or part (-m partial) of the file names in a target directory.

Requires the util-linux rename tool.

Warning

PLEASE consider making a backup of the target directory before running this script

Help documentation:

Syntax: batchRenameFiles.sh [-h|d|t|m]
Options:
h     Print this Help
d     Directory containing files to rename
t     Tab-delimited txt file with two columns:
        First column: old file names or old strings in file names
        Second column: new file names or new strings in file names
m     File rename mode [full|partial]

This script requires UNIX line endings for the -t names table. If you created your names table using Excel or a Windows computer, it may have DOS line endings. You can easily convert your table to the correct format using dos2unix.

Full replacement mode example:

# download the script
wget https://raw.githubusercontent.com/dmacguigan/SI-Ocean-DNA/refs/heads/main/scripts/utils/batchRenameFiles.sh
# make a test directory
mkdir full_test
# add some empty test files
touch full_test/S1.txt full_test/S2.txt full_test/S3.txt
# print contents of the test directory
ls -l full_test
# create a tab-delimited table of old and new file names
echo -e "S1.txt\tsample1.text" > names.txt
echo -e "S2.txt\tsample2.text" >> names.txt
echo -e "S3.txt\tsample3.text" >> names.txt
# check the table format
cat names.txt
# run the script
bash batchRenameFiles.sh -m full -d ./full_test -t names.txt
# print contents of the test directory
ls -l full_test

Partial replacement mode example:

Warning

Partial replacement mode may fail if strings to be replaced are nested. For example, if you want to replace “s_1” with “s_A” and “s_10” with “s_B”, you will end up with “s_A” and “s_A0”, because “s_1” is nested in “s_10”.

# download the script
wget https://raw.githubusercontent.com/dmacguigan/SI-Ocean-DNA/refs/heads/main/scripts/utils/batchRenameFiles.sh
# make a test directory
mkdir partial_test
# add some empty test files
touch partial_test/S1.txt partial_test/S2.txt partial_test/S3.txt partial_test/S1_S3.txt
# print contents of the test directory
ls -l partial_test
# create a tab-delimited table of old and new file names
echo -e "S1\tsample1" > names.txt
echo -e "S2\tsample2" >> names.txt
echo -e "S3\tsample3" >> names.txt
# check the table format
cat names.txt
# run the script
bash batchRenameFiles.sh -m partial -d ./partial_test -t names.txt
# print contents of the test directory
ls -l partial_test