dolomite-se 0.1.0a0

Save and load summarized experiments in the dolomite framework!

Save and load SummarizedExperiments in Python

Introduction

The dolomite-se package is the Python counterpart to the alabaster.se R package, providing methods for saving/reading SummarizedExperiment objects within the dolomite framework. All components of the SummarizedExperiment - assays, row data and column data - are saved to their respective file representations, which can be loaded in a new R/Python environment for cross-language analyses.

Quick start

Let's mock up a SummarizedExperiment:

import summarizedexperiment
import biocframe
import numpy

se = summarizedexperiment.SummarizedExperiment(
    assays={ "counts": numpy.random.rand(1000, 200) },
    row_data=biocframe.BiocFrame(
        { "foo": numpy.random.rand(1000) }, 
        row_names = ["gene" + str(i) for i in range(1000)]
    ),
    col_data=biocframe.BiocFrame(
        { "whee": numpy.random.rand(200) },
        row_names = ["cell" + str(i) for i in range(200)]
    )
)

Now we can save it:

from dolomite_base import stage_object, write_metadata
import dolomite_se

dir = "test"
meta = stage_object(se, dir, "mydata")
write_metadata(meta, dir)
print(meta["path"])
## mydata/experiment.json

And load it again, e,g., in a new session:

from dolomite_base import acquire_metadata, load_object

meta = acquire_metadata("test", "mydata/experiment.json")
reloaded = load_object(meta, dir)
## Class SummarizedExperiment with 1000 features and 200 samples
##   assays: ['counts']
##   row_data: ['foo']
##   col_data: ['whee']