Converting hdf5 to csv or tsv files

Question

I am looking for a sample code which can convert .h5 files to csv or tsv. I have to read .h5 and output should be csv or tsv.

Sample code would be much appreciated,p

Answer 1

Another python solution using pandas.

#!/usr/bin/env python3

import pandas as pd
import sys
fpath = sys.argv[1]
if len(sys.argv)>2:
    key = sys.argv[2]
    df = pd.read_hdf(fpath, key=key)
else:
    df = pd.read_hdf(fpath)

df.to_csv(sys.stdout, index=False)

This script is available here

First argument to this scrpt is hdf5 file. If second argument is passed, it is considered to be the name of column otherwise all columns are printed. It dumps the csv to stdout which you can redirect to a file.

For example, if your data is stored in hdf5 file called data.h5 and you have saved this script as hdf2df.py then

$ python3 hdf2df.py data.hf > data.csv

will write the data to a csv file data.csv.