h5df 0.0.3-dev

Library and CLI for storing numeric data frames in HDF5

Python library and CLI for storing numeric data frames in HDF5.

Rationale

Pandas has utilities for storing data frames in HDF5, but it uses PyTables under the hood, which means it is limited to frames with a relatively low number of columns (low 1000s).

This library is intended for storing and querying arbitrarily large numeric matrices which have row and column names. It has a CLI which can export/import to/from delimited text, or it can be used from within Python with tight integration with Pandas.

This library stores only numeric matrices, so it cannot handle data frames with mixed types (e.g., some strings and some numbers).

Installation

From PyPI:

pip install h5df

Latest version:

git clone https://github.com/gilesc/h5df.git
cd h5df
python setup.py install --user

This installs the CLI script “h5df”, and a Python module with the same name.

Usage

$ cat in.txt

    A   B   C
X   1   2   3
Y   4   5   5

$ h5df load foo.h5 /my/path < in.txt
$ h5df dump foo.h5 /my/path

    A   B   C
...

(more examples to come)

License

GPLv3