mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-19 19:08:11 +08:00
59f989d26f
* initial support for corpora schema conventions * remove debugging print * add corpora util module * tests * lint * PR review edits * PR changes * more PR changes * more PR chnages * PR fixes * formatting * PR updates * lint * PR review
662 lines
24 KiB
Python
662 lines
24 KiB
Python
"""
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This program converts an [AnnData H5AD](https://anndata.readthedocs.io/en/stable/)
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into a cellxgene TileDB structure, aka a [CXG](../../dev_docs/cxg.md).
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IF YOU UPDATE THIS FILE, IN ANY WAY THAT MODIFIES THE CXG FORMAT or CONTENTS,
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YOU MUST UPDATE THE CXG SPECIFICATION and VERSION NUMBER.
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"""
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import re
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import anndata
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import tiledb
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import argparse
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import numpy as np
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from os.path import splitext, basename
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import json
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from scipy.stats import mode
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from server.common.colors import convert_anndata_category_colors_to_cxg_category_colors
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from server.common.errors import ColorFormatException
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from server.common.corpora import (
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corpora_get_props_from_anndata,
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corpora_get_versions_from_anndata,
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corpora_is_version_supported,
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)
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# the CXG container version number. Must be a semver string (major.minor.patch)
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# DO NOT UPDATE THIS WITHOUT ALSO UPDATING THE CXG SPECIFICATION.
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CXG_VERSION = "0.2.0"
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# log_level must have a default
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log_level = 3
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def log(level, *args):
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global log_level
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if log_level and level <= log_level:
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print(*args)
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def main():
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parser = argparse.ArgumentParser()
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parser.add_argument("h5ad", nargs="?", help="H5AD file name")
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parser.add_argument(
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"--backed", action="store_true", help="loaded in file backed mode. Will be slower, but use less memory."
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)
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parser.add_argument(
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"--disable-custom-colors",
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action="store_true",
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default=False,
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help="Do not extract scanpy-compatible category colors from h5ad file.",
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)
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parser.add_argument(
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"--obs-names", help="Name of annotation to use for observations. If not specified, will use the obs index."
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)
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parser.add_argument(
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"--var-names", help="Name of annotation to use for variables. If not specified, will use the var index."
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)
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parser.add_argument("--verbose", "-v", action="count", default=0, help="verbose output")
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parser.add_argument("--title", help="Human readable dataset title. If omitted, will use filename")
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parser.add_argument(
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"--about",
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metavar="<URL>",
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help="URL providing more information about the dataset (hint: must be a fully specified absolute URL).",
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)
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parser.add_argument("--out", "--output", "-o", help="output CXG file name")
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parser.add_argument(
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"--sparse-threshold",
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"-s",
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type=float,
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default=0.0, # force dense by default
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help="The X array will be sparse if the percent of non-zeros falls below this value",
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)
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parser.add_argument(
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"--disable-corpora",
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action="store_true",
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default=False,
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help="Disable extraction and storing of Corpora schema information.",
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)
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args = parser.parse_args()
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global log_level
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log_level = args.verbose
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adata = anndata.read_h5ad(args.h5ad, backed="r" if args.backed else None)
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log(1, f"{basename(args.h5ad)} loaded...")
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basefname = splitext(basename(args.h5ad))[0]
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out = args.out if args.out is not None else basefname
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container = out if splitext(out)[1] == ".cxg" else out + ".cxg"
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corpora_props = load_corpora_props(args, adata) if not args.disable_corpora else None
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cxg_group_metadata = create_cxg_group_metadata(
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adata,
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basefname,
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title=args.title,
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about=args.about,
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corpora_props=corpora_props,
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extract_colors=not args.disable_custom_colors,
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)
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write_cxg(
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adata,
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container,
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cxg_group_metadata=cxg_group_metadata,
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var_names=args.var_names,
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obs_names=args.obs_names,
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sparse_threshold=args.sparse_threshold,
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)
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log(1, "done")
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def write_cxg(adata, container, cxg_group_metadata, var_names=None, obs_names=None, sparse_threshold=5.0):
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if not adata.var.index.is_unique:
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raise ValueError("Variable index is not unique - unable to convert.")
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if not adata.obs.index.is_unique:
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raise ValueError("Observation index is not unique - unable to convert.")
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"""
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TileDB bug TileDB-Inc/TileDB#1575 requires that we sanitize all column names
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prior to saving. This can be reverted when the bug is fixed.
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"""
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log(0, "Warning: sanitizing all dataframe column names.")
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clean_all_column_names(adata)
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ctx = tiledb.Ctx(
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{
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"sm.num_reader_threads": 32,
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"sm.num_writer_threads": 32,
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"sm.consolidation.buffer_size": 1 * 1024 * 1024 * 1024,
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}
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)
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tiledb.group_create(container, ctx=ctx)
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log(1, f"\t...group created, with name {container}")
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# dataset metadata
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save_metadata(container, cxg_group_metadata)
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log(1, "\t...dataset metadata saved")
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# var/gene dataframe
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save_dataframe(container, "var", adata.var, var_names, ctx=ctx)
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log(1, "\t...var dataframe created")
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# obs/cell dataframe
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save_dataframe(container, "obs", adata.obs, obs_names, ctx=ctx)
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log(1, "\t...obs dataframe created")
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# embeddings
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e_container = f"{container}/emb"
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tiledb.group_create(e_container, ctx=ctx)
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save_embeddings(e_container, adata, ctx)
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log(1, "\t...embeddings created")
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# X matrix
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save_X(container, adata.X, ctx, sparse_threshold)
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log(1, "\t...X created")
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"""
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TODO: the code used to handle type inferencing should not be duplicated between
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this tool and the server/common/utils code. When this tool is merged into
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the cellxgene CLI, consolidate.
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"""
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def dtype_to_schema(dtype):
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if dtype == np.float32:
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return (np.float32, {})
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elif dtype == np.int32:
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return (np.int32, {})
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elif dtype == np.bool_:
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return (np.uint8, {"type": "boolean"})
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elif dtype == np.str:
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return (np.unicode, {"type": "string"})
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elif dtype == "category":
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typ, hint = cxg_type(dtype.categories)
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return (typ, {"type": "categorical", "categories": dtype.categories.tolist()})
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else:
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raise TypeError(f"Annotations of type {dtype} are unsupported.")
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def _can_cast_to_float32(array):
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if array.dtype.kind == "f":
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# force downcast for all floats
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return True
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return False
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def _can_cast_to_int32(array):
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if array.dtype.kind in ["i", "u"]:
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if np.can_cast(array.dtype, np.int32):
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return True
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ii32 = np.iinfo(np.int32)
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if array.min() >= ii32.min and array.max() <= ii32.max:
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return True
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return False
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def cxg_type(array):
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try:
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return dtype_to_schema(array.dtype)
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except TypeError:
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dtype = array.dtype
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data_kind = dtype.kind
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if _can_cast_to_float32(array):
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return (np.float32, {})
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elif _can_cast_to_int32(array):
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return (np.int32, {})
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elif data_kind == "O" and dtype == "object":
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return (np.unicode, {"type": "string"})
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else:
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raise TypeError(f"Annotations of type {dtype} are unsupported.")
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def cxg_dtype(array):
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return cxg_type(array)[0]
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def create_dataframe(name, df, ctx):
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"""
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Current access patterns are oriented toward reading very large slices of
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the dataframe, one attribute at a time. Attribute data also tends to be
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(often) repetitive (bools, categories, strings).
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Given this, we use:
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* a large tile size (1000)
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* very aggressive compression levels
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"""
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filter = tiledb.FilterList(
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[
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# attempt aggressive compression as many of these dataframes are very repetitive
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# strings, bools and other non-float data.
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tiledb.ZstdFilter(level=22),
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]
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)
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attrs = [tiledb.Attr(name=col, dtype=cxg_dtype(df[col]), filters=filter) for col in df]
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domain = tiledb.Domain(tiledb.Dim(domain=(0, df.shape[0] - 1), tile=min(df.shape[0], 1000), dtype=np.uint32))
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schema = tiledb.ArraySchema(
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domain=domain, sparse=False, attrs=attrs, cell_order="row-major", tile_order="row-major"
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)
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tiledb.DenseArray.create(name, schema)
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def create_unique_column_name(df_cols, col_name_prefix):
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"""
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given the columns of a dataframe, and a name prefix, return a column name which
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does not exist in the dataframe, AND which is prefixed by `prefix`
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The approach is to append a numeric suffix, starting at zero and increasing by
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one, until an unused name is found (eg, prefix_0, prefix_1, ...).
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"""
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suffix = 0
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while f"{col_name_prefix}{suffix}" in df_cols:
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suffix += 1
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return f"{col_name_prefix}{suffix}"
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def alias_index_col(df, df_name, index_col_name):
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"""
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We rely in the existance of a unique, human-readable index for
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any dataframe (eg, var is typically gene name, obs the cell name).
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The user can specify these via the --obs-names and --var-names config.
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If they are not specified, use the existing index to create them, giving
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the resulting column a unique name (eg, "name").
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In both cases, enforce that the result is unique, and communicate the
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index column name via the 'index' field in the schema hints.
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"""
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if index_col_name is None:
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if not df.index.is_unique:
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raise KeyError(
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f"Values in {df_name}.index must be unique. "
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"Please prepare data to contain unique index values, or specify an "
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"alternative with --{ax_name}-name."
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)
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index_col_name = create_unique_column_name(df.columns, "name_")
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# turn the index into a normal column
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df.rename_axis(index_col_name, inplace=True)
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df.reset_index(inplace=True)
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elif index_col_name in df.columns:
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# User has specified alternative column for unique names, and it exists
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if not df[index_col_name].is_unique:
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raise KeyError(
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f"Values in {df_name}.{index_col_name} must be unique. Please prepare data to contain unique values."
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)
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else:
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raise KeyError(f"Annotation {index_col_name}, specified in --{df_name}-name, does not exist.")
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return (df, index_col_name)
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def save_dataframe(container, name, df, index_col_name, ctx):
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A_name = f"{container}/{name}"
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(df, index_col_name) = alias_index_col(df, name, index_col_name)
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create_dataframe(A_name, df, ctx=ctx)
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with tiledb.DenseArray(A_name, mode="w", ctx=ctx) as A:
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value = {}
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schema_hints = {}
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for k, v in df.items():
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dtype, hints = cxg_type(v)
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value[k] = v.to_numpy(dtype=dtype)
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if hints:
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schema_hints.update({k: hints})
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schema_hints.update({"index": index_col_name})
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A[:] = value
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A.meta["cxg_schema"] = json.dumps(schema_hints)
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tiledb.consolidate(A_name, ctx=ctx)
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def create_emb(e_name, emb):
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"""
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Embeddings are typically accessed with very large slices (or all of the embedding),
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and do not benefit from overly aggressive compression due to their format. Given
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this, we use:
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* large tile size (1000)
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* default compression level
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"""
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filters = tiledb.FilterList([tiledb.ZstdFilter()])
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attrs = [tiledb.Attr(dtype=emb.dtype, filters=filters)]
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dims = []
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for d in range(emb.ndim):
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shape = emb.shape
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dims.append(tiledb.Dim(domain=(0, shape[d] - 1), tile=min(shape[d], 1000), dtype=np.uint32))
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domain = tiledb.Domain(*dims)
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schema = tiledb.ArraySchema(
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domain=domain, sparse=False, attrs=attrs, capacity=1_000_000, cell_order="row-major", tile_order="row-major"
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)
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tiledb.DenseArray.create(e_name, schema)
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def is_valid_embedding(adata, name, arr):
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""" return True if this layout data is a valid array for front-end presentation:
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* ndarray, with shape (n_obs, >= 2), dtype float/int/uint
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* follows ScanPy embedding naming conventions
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* with all values finite or NaN (no +Inf or -Inf)
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"""
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is_valid = type(name) == str and name.startswith("X_") and len(name) > 2
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is_valid = is_valid and type(arr) == np.ndarray and arr.dtype.kind in "fiu"
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is_valid = is_valid and arr.shape[0] == adata.n_obs and arr.shape[1] >= 2
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is_valid = is_valid and not np.any(np.isinf(arr)) and not np.all(np.isnan(arr))
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return is_valid
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def save_embeddings(container, adata, ctx):
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for (name, value) in adata.obsm.items():
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if is_valid_embedding(adata, name, value):
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e_name = f"{container}/{name[2:]}"
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create_emb(e_name, value)
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with tiledb.DenseArray(e_name, mode="w", ctx=ctx) as A:
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A[:] = value
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tiledb.consolidate(e_name, ctx=ctx)
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log(1, f"\t\t...{name} embedding created")
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def create_X(X_name, shape, is_sparse):
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"""
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The X matrix is accessed in both row and column oriented patterns, depending on the
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particular operation. Because of the data type, default compression works best.
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The tile size, (50, 100) for dense, and (512,2048) for sparse,
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and global layout (row/col) was chosen empirically, by benchmarking
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the current cellxgene backend.
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"""
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filters = tiledb.FilterList([tiledb.ZstdFilter()])
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attrs = [tiledb.Attr(dtype=np.float32, filters=filters)]
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if is_sparse:
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domain = tiledb.Domain(
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tiledb.Dim(name="obs", domain=(0, shape[0] - 1), tile=min(shape[0], 512), dtype=np.uint32),
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tiledb.Dim(name="var", domain=(0, shape[1] - 1), tile=min(shape[1], 2048), dtype=np.uint32),
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)
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else:
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domain = tiledb.Domain(
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tiledb.Dim(name="obs", domain=(0, shape[0] - 1), tile=min(shape[0], 50), dtype=np.uint32),
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tiledb.Dim(name="var", domain=(0, shape[1] - 1), tile=min(shape[1], 100), dtype=np.uint32),
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)
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schema = tiledb.ArraySchema(
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domain=domain, sparse=is_sparse, attrs=attrs, cell_order="row-major", tile_order="col-major"
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)
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if is_sparse:
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tiledb.SparseArray.create(X_name, schema)
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else:
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tiledb.DenseArray.create(X_name, schema)
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def evaluate_for_sparse_encoding(xdata, sparse_threshold):
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"""
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This function determines if the X matrix has a sparsity below the sparse_threshold.
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This function also returns the number of non-zeros encountered and number
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of elements evaluated. This function may return before evaluating the whole X matrix
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if it can be determined that X is not sparse enough.
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"""
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shape = xdata.shape
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stride = min(int(np.power(10, np.around(np.log10(1e9 / shape[1])))), 10_000)
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nnz = 0
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maxnnz = int(shape[0] * shape[1] * sparse_threshold / 100)
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for row in range(0, shape[0], stride):
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lim = min(row + stride, shape[0])
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a = xdata[row:lim, :]
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if type(a) is not np.ndarray:
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a = a.toarray()
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nnz += np.count_nonzero(a)
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if nnz > maxnnz:
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return (False, nnz, lim * shape[1])
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log(2, "\t...rows", lim, "of", shape[0], "nnz", nnz, "nnz percent %5.2f%%" % (100 * nnz / (lim * shape[1])))
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is_sparse = (100.0 * nnz / (shape[0] * shape[1])) < sparse_threshold
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return (is_sparse, nnz, shape[0] * shape[1])
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def evaluate_for_sparse_column_shift_encoding(xdata, sparse_threshold):
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"""Column shift encoding works by taking the most common value in each column, then
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subtracting that value from each element of the column. If each column mostly contains
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its most common value, then the resulting matrix can be very sparse.
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This function determines if column shift encoding can be used to transform
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the X matrix into a sparse matrix with a sparsity below the sparse_threshold.
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If so, return the col_shift array that stores this encoding.
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This function also returns the number of non-zeros encountered and number
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of elements evaluated. This function may return before evaluating the whole X matrix
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if it can be determined that X cannot benefit from column shift encoding.
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"""
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shape = xdata.shape
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stride = max(1, 128_000_000 // shape[0])
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col_shift = np.zeros(shape[1])
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nnz = 0
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maxnnz = int(shape[0] * shape[1] * sparse_threshold / 100)
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for col in range(0, shape[1], stride):
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lim = min(col + stride, shape[1])
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a = xdata[:, col:lim]
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if type(a) is not np.ndarray:
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a = a.toarray()
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m = mode(a)
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col_shift[col:lim] = m.mode
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nnz += shape[0] * (lim - col) - np.sum(m.count)
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if nnz > maxnnz:
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return (None, nnz, shape[0] * lim)
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log(2, "\t...cols", lim, "of", shape[1], "nnz", nnz, "nnz percent %5.2f%%" % (100 * nnz / (lim * shape[0])))
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is_sparse = (100.0 * nnz / (shape[0] * shape[1])) < sparse_threshold
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return (col_shift if is_sparse else None, nnz, shape[0] * shape[1])
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def save_X(container, xdata, ctx, sparse_threshold, expect_sparse=False):
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# Save X count matrix
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X_name = f"{container}/X"
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shape = xdata.shape
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log(1, "\t...shape:", str(shape))
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col_shift = None
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if sparse_threshold == 100:
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is_sparse = True
|
|
elif sparse_threshold == 0:
|
|
is_sparse = False
|
|
else:
|
|
is_sparse, nnz, nelem = evaluate_for_sparse_encoding(xdata, sparse_threshold)
|
|
percent = 100.0 * nnz / nelem
|
|
if nelem != shape[0] * shape[1]:
|
|
log(1, "\t...sparse=", is_sparse, "non-zeros percent (estimate): %6.2f" % percent)
|
|
else:
|
|
log(1, "\t...sparse=", is_sparse, "non-zeros:", nnz, "percent: %6.2f" % percent)
|
|
|
|
is_sparse = percent < sparse_threshold
|
|
if not is_sparse:
|
|
col_shift, nnz, nelem = evaluate_for_sparse_column_shift_encoding(xdata, sparse_threshold)
|
|
is_sparse = col_shift is not None
|
|
percent = 100.0 * nnz / nelem
|
|
if nelem != shape[0] * shape[1]:
|
|
log(1, "\t...sparse=", is_sparse, "col shift non-zeros percent (estimate): %6.2f" % percent)
|
|
else:
|
|
log(1, "\t...sparse=", is_sparse, "col shift non-zeros:", nnz, "percent: %6.2f" % percent)
|
|
|
|
if expect_sparse is True and is_sparse is False:
|
|
return False
|
|
|
|
create_X(X_name, shape, is_sparse)
|
|
stride = min(int(np.power(10, np.around(np.log10(1e9 / shape[1])))), 10_000)
|
|
if is_sparse:
|
|
if col_shift is not None:
|
|
log(1, "\t...output X as sparse matrix with column shift encoding")
|
|
X_col_shift_name = f"{container}/X_col_shift"
|
|
filters = tiledb.FilterList([tiledb.ZstdFilter()])
|
|
attrs = [tiledb.Attr(dtype=np.float32, filters=filters)]
|
|
domain = tiledb.Domain(tiledb.Dim(domain=(0, shape[1] - 1), tile=min(shape[1], 5000), dtype=np.uint32))
|
|
schema = tiledb.ArraySchema(domain=domain, attrs=attrs)
|
|
tiledb.DenseArray.create(X_col_shift_name, schema)
|
|
with tiledb.DenseArray(X_col_shift_name, mode="w", ctx=ctx) as X_col_shift:
|
|
X_col_shift[:] = col_shift
|
|
tiledb.consolidate(X_col_shift_name, ctx=ctx)
|
|
else:
|
|
log(1, "\t...output X as sparse matrix")
|
|
|
|
with tiledb.SparseArray(X_name, mode="w", ctx=ctx) as X:
|
|
nnz = 0
|
|
for row in range(0, shape[0], stride):
|
|
lim = min(row + stride, shape[0])
|
|
a = xdata[row:lim, :]
|
|
if type(a) is not np.ndarray:
|
|
a = a.toarray()
|
|
if col_shift is not None:
|
|
a = a - col_shift
|
|
indices = np.nonzero(a)
|
|
trow = indices[0] + row
|
|
nnz += indices[0].shape[0]
|
|
X[trow, indices[1]] = a[indices[0], indices[1]]
|
|
log(2, "\t...rows", lim, "of", shape[0], "nnz", nnz, "sparse", nnz / (lim * shape[1]))
|
|
|
|
else:
|
|
log(1, "\t...output X as dense matrix")
|
|
with tiledb.DenseArray(X_name, mode="w", ctx=ctx) as X:
|
|
for row in range(0, shape[0], stride):
|
|
lim = min(row + stride, shape[0])
|
|
a = xdata[row:lim, :]
|
|
if type(a) is not np.ndarray:
|
|
a = a.toarray()
|
|
X[row:lim, :] = a
|
|
log(2, "\t...rows", row, "to", lim)
|
|
|
|
tiledb.consolidate(X_name, ctx=ctx)
|
|
if hasattr(tiledb, "vacuum"):
|
|
tiledb.vacuum(X_name)
|
|
|
|
return is_sparse
|
|
|
|
|
|
def save_metadata(container, metadata_dict):
|
|
"""
|
|
Save all dataset-wide metadata. This includes:
|
|
* CXG version
|
|
* dataset metadata, such as title and about link.
|
|
|
|
Longer term, tiledb will have support for metadata on groups. Until
|
|
such feature exists, create an empty array and annotate that array.
|
|
|
|
https://github.com/TileDB-Inc/TileDB-Py/issues/254
|
|
"""
|
|
a_name = f"{container}/cxg_group_metadata"
|
|
with tiledb.from_numpy(a_name, np.zeros((1,))) as A:
|
|
pass
|
|
with tiledb.DenseArray(a_name, mode="w") as A:
|
|
for k, v in metadata_dict.items():
|
|
A.meta[k] = v
|
|
|
|
|
|
def load_corpora_props(args, adata):
|
|
versions = corpora_get_versions_from_anndata(adata)
|
|
if versions is None:
|
|
return None
|
|
|
|
[corpora_schema_version, corpora_encoding_version] = versions
|
|
corpora_props = corpora_get_props_from_anndata(adata)
|
|
version_is_supported = corpora_is_version_supported(corpora_schema_version, corpora_encoding_version)
|
|
if not version_is_supported or not corpora_props:
|
|
log(0, "ERROR: Unknown source file schema version is unsupported")
|
|
raise ValueError("Unsupported Corpora schema version")
|
|
|
|
log(1, "FYI, file appears to be encoded using Corpora schema standards...")
|
|
if args.title is not None or args.about is not None:
|
|
log(0, "Warning: explicit specification of --title or --about will override Corpora schema fields.")
|
|
|
|
return corpora_props
|
|
|
|
|
|
def create_cxg_group_metadata(adata, basefname, title=None, about=None, corpora_props=None, extract_colors=True):
|
|
|
|
if corpora_props is not None:
|
|
# clobber encoding version to be OUR version, not the source H5AD encoding
|
|
corpora_props["version"].update({"corpora_encoding_version": CXG_VERSION})
|
|
corpora_project_links = corpora_props.get("project_links", [])
|
|
corpora_about_link = next(
|
|
(link for link in corpora_project_links if (link.get("link_type", None) == "SUMMARY")), {}
|
|
)
|
|
else:
|
|
corpora_about_link = {}
|
|
|
|
title = title or corpora_about_link.get("link_name", basefname)
|
|
about = about or corpora_about_link.get("link_url")
|
|
|
|
cxg_group_metadata = {"cxg_version": CXG_VERSION, "cxg_properties": json.dumps({"title": title, "about": about})}
|
|
if corpora_props is not None:
|
|
cxg_group_metadata.update({"corpora": json.dumps(corpora_props)})
|
|
|
|
if extract_colors:
|
|
try:
|
|
cxg_group_metadata["cxg_category_colors"] = json.dumps(
|
|
convert_anndata_category_colors_to_cxg_category_colors(adata)
|
|
)
|
|
except ColorFormatException:
|
|
log(
|
|
0,
|
|
"Warning: failed to extract colors from h5ad file! "
|
|
"Fix the h5ad file or rerun with --disable-custom-colors. See help for details.",
|
|
)
|
|
|
|
return cxg_group_metadata
|
|
|
|
|
|
def sanitize_keys(keys):
|
|
"""
|
|
We need names to be safe to use as attribute names in tiledb. See:
|
|
TileDB-Inc/TileDB#1575
|
|
TileDB-Inc/TileDB-Py#294
|
|
This can be entirely removed once they add proper escaping.
|
|
|
|
Args: list of keys
|
|
Returns: dict of {old_key: new_key, ...}
|
|
|
|
Returned new keys will be both safe and unique.
|
|
|
|
Masking out [~/.] and anything outside the ASCII range.
|
|
"""
|
|
p = re.compile(r"[^ -\.0-\[\]-\}]")
|
|
clean_keys = {k: p.sub("_", k) for k in keys}
|
|
|
|
used_keys = set()
|
|
clean_unique_keys = {}
|
|
for k, v in clean_keys.items():
|
|
if v not in used_keys:
|
|
used_keys.add(v)
|
|
clean_unique_keys[k] = v
|
|
continue
|
|
|
|
# else, needs deduping.
|
|
counter = 1
|
|
while True:
|
|
candidate_name = v + "-" + str(counter)
|
|
if candidate_name not in used_keys:
|
|
used_keys.add(candidate_name)
|
|
clean_unique_keys[k] = candidate_name
|
|
break
|
|
counter += 1
|
|
|
|
for k, v, in clean_unique_keys.items():
|
|
if k != v:
|
|
log(1, f"Renaming {k} to {v}")
|
|
return clean_unique_keys
|
|
|
|
|
|
def sanitize_df(df):
|
|
df.rename(columns=sanitize_keys(df.keys().tolist()), inplace=True)
|
|
|
|
|
|
def sanitize_mapping(mapping):
|
|
clean_keys = sanitize_keys([k for k in mapping.keys()])
|
|
for old_key, new_key in clean_keys.items():
|
|
if old_key != new_key:
|
|
mapping[new_key] = mapping[old_key]
|
|
del mapping[old_key]
|
|
|
|
|
|
def clean_all_column_names(adata):
|
|
sanitize_df(adata.obs)
|
|
sanitize_df(adata.var)
|
|
sanitize_mapping(adata.obsm)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|