hdf5array

Introduction

This is the Python equivalent of Bioconductor’s HDF5Array package, providing a representation of HDF5-backed arrays within the delayedarray framework. The idea is to allow users to store, manipulate and operate on large datasets without loading them into memory, in a manner that is trivially compatible with other data structures in the BiocPy ecosystem.

Installation

This package can be installed from PyPI with the usual commands:

pip install hdf5array

Quick start

Let’s mock up a dense array:

import numpy
data = numpy.random.rand(40, 50, 100)

import h5py
with h5py.File("whee.h5", "w") as handle:
    handle.create_dataset("yay", data=data)

We can now represent it as a Hdf5DenseArray:

import hdf5array
arr = hdf5array.Hdf5DenseArray("whee.h5", "yay", native_order=True)
## <40 x 50 x 100> Hdf5DenseArray object of type 'float64'
## [[[0.63008796, 0.34849183, 0.75621679, ..., 0.07343495, 0.63095765,
##    0.625732  ],
##   [0.68123095, 0.91403054, 0.74737122, ..., 0.17344344, 0.82254404,
##    0.58158815],
##   [0.83287116, 0.40738123, 0.89887551, ..., 0.34936481, 0.76600276,
##    0.91991967],
##   ...,

This is just a subclass of a DelayedArray and can be used anywhere in the BiocPy framework. Parts of the NumPy API are also supported - for example, we could apply a variety of delayed operations:

scaling = numpy.random.rand(100)
transformed = numpy.log1p(arr / scaling)
## <40 x 50 x 100> DelayedArray object of type 'float64'
## [[[0.58803887, 0.3458478 , 0.82700531, ..., 0.08224734, 0.65678967,
##    0.56893312],
##   [0.62348907, 0.7341526 , 0.82040225, ..., 0.18437718, 0.7932422 ,
##    0.53784637],
##   [0.72176703, 0.39407341, 0.92788307, ..., 0.34205035, 0.75487196,
##    0.75456938],
##   ...,

Check out the documentation for more details.

Handling sparse matrices

We support a variety of compressed sparse formats where the non-zero elements are held inside three separate datasets - usually data, indices and indptr, based on the 10X Genomics sparse HDF5 format. To demonstrate, let’s mock up some sparse data using scipy:

import scipy.sparse
mock = scipy.sparse.random(1000, 200, 0.1).tocsc()

with h5py.File("sparse_whee.h5", "w") as handle:
    handle.create_dataset("sparse_blah/data", data=mock.data, compression="gzip")
    handle.create_dataset("sparse_blah/indices", data=mock.indices, compression="gzip")
    handle.create_dataset("sparse_blah/indptr", data=mock.indptr, compression="gzip")

We can then create a sparse HDF5-backed matrix. Note that there is some variation in this HDF5 compressed sparse format, notably where the dimensions are stored and whether it is column/row-major. The constructor will not do any auto-detection so we need to provide this information explicitly:

import hdf5array
arr = hdf5array.Hdf5CompressedSparseMatrix(
    "sparse_whee.h5",
    "sparse_blah",
    shape=(100, 200),
    by_column=True
)
## <100 x 200> sparse Hdf5CompressedSparseMatrix object of type 'float64'
## [[0.        , 0.        , 0.26563417, ..., 0.        , 0.        ,
##   0.        ],
##  [0.        , 0.        , 0.        , ..., 0.23896924, 0.        ,
##   0.        ],
##  [0.        , 0.        , 0.        , ..., 0.42236848, 0.3585153 ,
##   0.        ],
##  ...,
##  [0.        , 0.        , 0.3363087 , ..., 0.        , 0.        ,
##   0.        ],
##  [0.        , 0.        , 0.        , ..., 0.        , 0.        ,
##   0.        ],
##  [0.        , 0.        , 0.        , ..., 0.        , 0.        ,
##   0.        ]]