/pytables-mapping

Primary LanguagePythonMIT LicenseMIT

Pytables-mapping

Checked with mypy

Pytables-mapping - a simple mapping for pytables objects: tables, arrays, complex custom structures.

Inspired by Django ORM and SimpleTable

Installation

Install and update using pip:

pip install git+https://github.com/antonkonovalov1976/pytables-mapping.git -U

Requirements

  • Python 3.6+
  • A supported version of PyTables 3.7

A simple example:

import numpy as np
import pytables_mapping as mapping

class PythagoreanTriplesTable(mapping.Table):
    """Pythagorean triples table."""
    FULL_NODE_PATH = '/sequences'
    OBJECT_NAME = 'pythagorean_triples'
    DESCRIPTION = np.dtype([
        ('A', np.int64),
        ('B', np.int64),
        ('C', np.int64)])

class MainStore(mapping.HDF5Store):
    STORE_VERSION = 1
    pythagorean_triples = PythagoreanTriplesTable()

if __name__ == '__main__':
    with MainStore('data.h5') as store:
        print(store.pythagorean_triples.read())

N.B.

To choose correct compression options see: http://www.pytables.org/usersguide/libref/helper_classes.html#the-filters-class

and benchmarks: http://alimanfoo.github.io/2016/09/21/genotype-compression-benchmark.html

LINKS