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#!/usr/bin/env python | |
# ================================================================ | |
# This script demonstrates some issues for tiledbsoma-py for GitHub | |
# issue https://github.com/single-cell-data/TileDB-SOMA/issues/2822. | |
# These are issues: | |
# | |
# * Involving tiledbsoma.io.from_anndata / tiledbsoma.io.from_h5ad, | |
# and not tiledbsoma.Experiment.add_new_dataframe. (Those issues | |
# will be separately discussed.) | |
# * Involving various kinds of "null" -- Python None, pd.NA, math.nan -- | |
# contained within AnnData input objects | |
# * Involving column types of categorical-of-string, bool, and int. | |
# ================================================================ | |
import tiledbsoma | |
import tiledb | |
import sys | |
# ================================================================ | |
if len(sys.argv) == 2: | |
uri = sys.argv[1] | |
else: | |
print("Need URI as argument.") | |
sys.exit(1) | |
sep = "-" * 64 | |
with tiledb.open(uri) as A: | |
print() | |
print(sep) | |
print("OBS TILEDB-PY SCHEMA:") | |
print() | |
print(A.schema) | |
print() | |
print(sep) | |
print("OBS TILEDB-PY READ:") | |
print() | |
print(A.df[:]) | |
print() | |
with tiledbsoma.DataFrame.open(uri) as obs: | |
print() | |
print(sep) | |
print("OBS TILEDB-SOMA SCHEMA:") | |
print() | |
print(obs.schema) | |
print() | |
print(sep) | |
print("OBS TILEDB-SOMA READ ARROW:") | |
print() | |
print(obs.read().concat()) | |
print() | |
print(sep) | |
print("OBS TILEDB-SOMA READ PANDAS:") | |
print() | |
print(obs.read().concat().to_pandas()) |
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