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johnkerl committed Jun 22, 2022
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13 changes: 7 additions & 6 deletions apis/python/examples/uniformizer.py
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#!/usr/bin/env python

"""
The following is an example of uniformizing multiple datasets into a SOMA collection. This is a
simple example that assumes all source H5ADs comply with the [cellxgene 2.0
schema](https://pypi.org/project/cellxgene-schema/), although you can modify this to conform
with your own organization's schema.
The following shows an example of how to take multiple H5AD files and add them to a single SOMA
Collection. This is a simple example that assumes all source H5ADs comply with the [cellxgene 2.0
schema](https://pypi.org/project/cellxgene-schema/), although you can modify this to conform with
your own organization's schema.
To keep the example simple, any data outside that schema are discarded. The example peforms three
steps:
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Examples:
python uniformizer.py -v atlas2 add-h5ad data1.h5ad
python uniformizer.py -v atlas2 add-soma soma2
python uniformizer.py -v atlas add-h5ad data1.h5ad
python uniformizer.py -v atlas add-h5ad data2.h5ad
python uniformizer.py -v atlas add-soma soma3 # If you've already ingested into a separate SOMA
Note: This code for populating an atlas is independent of querying an atlas. See also
[https://github.com/single-cell-data/TileDB-SingleCell](https://github.com/single-cell-data/TileDB-SingleCell)
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