Extracting data and saving data from hdf5
You can always try using the h5py module in Python.

import h5py

# Load existing file
filename = "myfile.hdf5"
dataset = h5py.File(filename, "r")

# Show keys
[print(item) for item in dataset.items()]

# Assuming that you want to select the first 10 rows of key "A"
data = dataset["A"][:10]
dataset.close()

# Create the new dataset / file
dataset2 = h5py.File("myfile2.hdf5", "w")
dataset2.create_dataset("A", data)
dataset2.close()