Quick example of renaming files in nested directory structure

rename.py

# Renames all files using name of directory.
# e.g. sample_name_1/s_1_sequence.txt.gz -> sample_name_1_s_1_sequence.txt.gz

import glob
import shutil

filepaths = glob.glob("sample_name_*/s_*_sequence.txt.gz")
new_names = [x.replace("/", "_") for x in filepaths]
[shutil.copyfile(x[0], x[1]) for x in zip(filepaths, new_names)]

setup.sh

#!/bin/bash

# Set up a directory with files in the following format:
#
#                     - s_1_sequence.txt.gz
#   - sample_name_1 --
#                     - s_2_sequence.txt.gz
#
# --
#
#                     - s_1_sequence.txt.gz
#   - sample_name_2 --
#                     - s_2_sequence.txt.gz
#

mkdir sample_name_{1..9}

for dir in sample_name_*
do
  touch $dir/s_{1..3}_sequence.txt.gz
done