sclab 0.1.7__py3-none-any.whl → 0.3.4__py3-none-any.whl

sclab/scanpy/readwrite.py

@@ -0,0 +1,1108 @@
+"""Reading and Writing"""
+
+from __future__ import annotations
+
+import json
+from enum import Enum
+from pathlib import Path, PurePath
+from typing import TYPE_CHECKING
+
+import anndata.utils
+import h5py
+import numpy as np
+import pandas as pd
+from packaging.version import Version
+
+if Version(anndata.__version__) >= Version("0.11.0rc2"):
+    from anndata.io import (
+        read_csv,
+        read_excel,
+        read_h5ad,
+        read_hdf,
+        read_loom,
+        read_mtx,
+        read_text,
+    )
+else:
+    from anndata import (
+        read_csv,
+        read_excel,
+        read_h5ad,
+        read_hdf,
+        read_loom,
+        read_mtx,
+        read_text,
+    )
+from anndata import AnnData
+from matplotlib.image import imread
+
+from . import logging as logg
+from ._compat import old_positionals
+from ._settings import settings
+
+
+class Empty(Enum):
+    token = 0
+
+    def __repr__(self) -> str:
+        return "_empty"
+
+
+_empty = Empty.token
+
+
+if TYPE_CHECKING:
+    from typing import BinaryIO, Literal
+
+    # from ._utils import Empty
+
+# .gz and .bz2 suffixes are also allowed for text formats
+text_exts = {
+    "csv",
+    "tsv",
+    "tab",
+    "data",
+    "txt",  # these four are all equivalent
+}
+avail_exts = {
+    "anndata",
+    "xlsx",
+    "h5",
+    "h5ad",
+    "mtx",
+    "mtx.gz",
+    "soft.gz",
+    "loom",
+} | text_exts
+"""Available file formats for reading data. """
+
+
+# --------------------------------------------------------------------------------
+# Reading and Writing data files and AnnData objects
+# --------------------------------------------------------------------------------
+
+
+@old_positionals(
+    "sheet",
+    "ext",
+    "delimiter",
+    "first_column_names",
+    "backup_url",
+    "cache",
+    "cache_compression",
+)
+def read(
+    filename: Path | str,
+    backed: Literal["r", "r+"] | None = None,
+    *,
+    sheet: str | None = None,
+    ext: str | None = None,
+    delimiter: str | None = None,
+    first_column_names: bool = False,
+    backup_url: str | None = None,
+    cache: bool = False,
+    cache_compression: Literal["gzip", "lzf"] | None | Empty = _empty,
+    **kwargs,
+) -> AnnData:
+    """\
+    Read file and return :class:`~anndata.AnnData` object.
+
+    To speed up reading, consider passing ``cache=True``, which creates an hdf5
+    cache file.
+
+    Parameters
+    ----------
+    filename
+        If the filename has no file extension, it is interpreted as a key for
+        generating a filename via ``sc.settings.writedir / (filename +
+        sc.settings.file_format_data)``.  This is the same behavior as in
+        ``sc.read(filename, ...)``.
+    backed
+        If ``'r'``, load :class:`~anndata.AnnData` in ``backed`` mode instead
+        of fully loading it into memory (`memory` mode). If you want to modify
+        backed attributes of the AnnData object, you need to choose ``'r+'``.
+    sheet
+        Name of sheet/table in hdf5 or Excel file.
+    ext
+        Extension that indicates the file type. If ``None``, uses extension of
+        filename.
+    delimiter
+        Delimiter that separates data within text file. If ``None``, will split at
+        arbitrary number of white spaces, which is different from enforcing
+        splitting at any single white space ``' '``.
+    first_column_names
+        Assume the first column stores row names. This is only necessary if
+        these are not strings: strings in the first column are automatically
+        assumed to be row names.
+    backup_url
+        Retrieve the file from an URL if not present on disk.
+    cache
+        If `False`, read from source, if `True`, read from fast 'h5ad' cache.
+    cache_compression
+        See the h5py :ref:`dataset_compression`.
+        (Default: `settings.cache_compression`)
+    kwargs
+        Parameters passed to :func:`~anndata.io.read_loom`.
+
+    Returns
+    -------
+    An :class:`~anndata.AnnData` object
+    """
+    filename = Path(filename)  # allow passing strings
+    if is_valid_filename(filename):
+        return _read(
+            filename,
+            backed=backed,
+            sheet=sheet,
+            ext=ext,
+            delimiter=delimiter,
+            first_column_names=first_column_names,
+            backup_url=backup_url,
+            cache=cache,
+            cache_compression=cache_compression,
+            **kwargs,
+        )
+    # generate filename and read to dict
+    filekey = str(filename)
+    filename = settings.writedir / (filekey + "." + settings.file_format_data)
+    if not filename.exists():
+        raise ValueError(
+            f"Reading with filekey {filekey!r} failed, "
+            f"the inferred filename {filename!r} does not exist. "
+            "If you intended to provide a filename, either use a filename "
+            f"ending on one of the available extensions {avail_exts} "
+            "or pass the parameter `ext`."
+        )
+    return read_h5ad(filename, backed=backed)
+
+
+@old_positionals("genome", "gex_only", "backup_url")
+def read_10x_h5(
+    filename: Path | str,
+    *,
+    genome: str | None = None,
+    gex_only: bool = True,
+    backup_url: str | None = None,
+) -> AnnData:
+    """\
+    Read 10x-Genomics-formatted hdf5 file.
+
+    Parameters
+    ----------
+    filename
+        Path to a 10x hdf5 file.
+    genome
+        Filter expression to genes within this genome. For legacy 10x h5
+        files, this must be provided if the data contains more than one genome.
+    gex_only
+        Only keep 'Gene Expression' data and ignore other feature types,
+        e.g. 'Antibody Capture', 'CRISPR Guide Capture', or 'Custom'
+    backup_url
+        Retrieve the file from an URL if not present on disk.
+
+    Returns
+    -------
+    Annotated data matrix, where observations/cells are named by their
+    barcode and variables/genes by gene name. Stores the following information:
+
+    :attr:`~anndata.AnnData.X`
+        The data matrix is stored
+    :attr:`~anndata.AnnData.obs_names`
+        Cell names
+    :attr:`~anndata.AnnData.var_names`
+        Gene names for a feature barcode matrix, probe names for a probe bc matrix
+    :attr:`~anndata.AnnData.var`\\ `['gene_ids']`
+        Gene IDs
+    :attr:`~anndata.AnnData.var`\\ `['feature_types']`
+        Feature types
+    :attr:`~anndata.AnnData.obs`\\ `[filtered_barcodes]`
+        filtered barcodes if present in the matrix
+    :attr:`~anndata.AnnData.var`
+        Any additional metadata present in /matrix/features is read in.
+    """
+    start = logg.info(f"reading {filename}")
+    is_present = _check_datafile_present_and_download(filename, backup_url=backup_url)
+    if not is_present:
+        logg.debug(f"... did not find original file {filename}")
+    with h5py.File(str(filename), "r") as f:
+        v3 = "/matrix" in f
+    if v3:
+        adata = _read_v3_10x_h5(filename, start=start)
+        if genome:
+            if genome not in adata.var["genome"].values:
+                raise ValueError(
+                    f"Could not find data corresponding to genome '{genome}' in '{filename}'. "
+                    f"Available genomes are: {list(adata.var['genome'].unique())}."
+                )
+            adata = adata[:, adata.var["genome"] == genome]
+        if gex_only:
+            adata = adata[:, adata.var["feature_types"] == "Gene Expression"]
+        if adata.is_view:
+            adata = adata.copy()
+    else:
+        adata = _read_legacy_10x_h5(filename, genome=genome, start=start)
+    return adata
+
+
+def _read_legacy_10x_h5(filename, *, genome=None, start=None):
+    """
+    Read hdf5 file from Cell Ranger v2 or earlier versions.
+    """
+    with h5py.File(str(filename), "r") as f:
+        try:
+            children = list(f.keys())
+            if not genome:
+                if len(children) > 1:
+                    raise ValueError(
+                        f"'{filename}' contains more than one genome. For legacy 10x h5 "
+                        "files you must specify the genome if more than one is present. "
+                        f"Available genomes are: {children}"
+                    )
+                genome = children[0]
+            elif genome not in children:
+                raise ValueError(
+                    f"Could not find genome '{genome}' in '{filename}'. "
+                    f"Available genomes are: {children}"
+                )
+
+            dsets = {}
+            _collect_datasets(dsets, f[genome])
+
+            # AnnData works with csr matrices
+            # 10x stores the transposed data, so we do the transposition right away
+            from scipy.sparse import csr_matrix
+
+            M, N = dsets["shape"]
+            data = dsets["data"]
+            if dsets["data"].dtype == np.dtype("int32"):
+                data = dsets["data"].view("float32")
+                data[:] = dsets["data"]
+            matrix = csr_matrix(
+                (data, dsets["indices"], dsets["indptr"]),
+                shape=(N, M),
+            )
+            # the csc matrix is automatically the transposed csr matrix
+            # as scanpy expects it, so, no need for a further transpostion
+            adata = AnnData(
+                matrix,
+                obs=dict(obs_names=dsets["barcodes"].astype(str)),
+                var=dict(
+                    var_names=dsets["gene_names"].astype(str),
+                    gene_ids=dsets["genes"].astype(str),
+                ),
+            )
+            logg.info("", time=start)
+            return adata
+        except KeyError:
+            raise Exception("File is missing one or more required datasets.")
+
+
+def _collect_datasets(dsets: dict, group: h5py.Group):
+    for k, v in group.items():
+        if isinstance(v, h5py.Dataset):
+            dsets[k] = v[()]
+        else:
+            _collect_datasets(dsets, v)
+
+
+def _read_v3_10x_h5(filename, *, start=None):
+    """
+    Read hdf5 file from Cell Ranger v3 or later versions.
+    """
+    with h5py.File(str(filename), "r") as f:
+        try:
+            dsets = {}
+            _collect_datasets(dsets, f["matrix"])
+
+            from scipy.sparse import csr_matrix
+
+            M, N = dsets["shape"]
+            data = dsets["data"]
+            if dsets["data"].dtype == np.dtype("int32"):
+                data = dsets["data"].view("float32")
+                data[:] = dsets["data"]
+            matrix = csr_matrix(
+                (data, dsets["indices"], dsets["indptr"]),
+                shape=(N, M),
+            )
+            obs_dict = {"obs_names": dsets["barcodes"].astype(str)}
+            var_dict = {"var_names": dsets["name"].astype(str)}
+
+            if "gene_id" not in dsets:
+                # Read metadata specific to a feature-barcode matrix
+                var_dict["gene_ids"] = dsets["id"].astype(str)
+            else:
+                # Read metadata specific to a probe-barcode matrix
+                var_dict.update(
+                    {
+                        "gene_ids": dsets["gene_id"].astype(str),
+                        "probe_ids": dsets["id"].astype(str),
+                    }
+                )
+            var_dict["feature_types"] = dsets["feature_type"].astype(str)
+            if "filtered_barcodes" in f["matrix"]:
+                obs_dict["filtered_barcodes"] = dsets["filtered_barcodes"].astype(bool)
+
+            if "features" in f["matrix"]:
+                var_dict.update(
+                    (
+                        feature_metadata_name,
+                        dsets[feature_metadata_name].astype(
+                            bool if feature_metadata_item.dtype.kind == "b" else str
+                        ),
+                    )
+                    for feature_metadata_name, feature_metadata_item in f["matrix"][
+                        "features"
+                    ].items()
+                    if isinstance(feature_metadata_item, h5py.Dataset)
+                    and feature_metadata_name
+                    not in [
+                        "name",
+                        "feature_type",
+                        "id",
+                        "gene_id",
+                        "_all_tag_keys",
+                    ]
+                )
+            else:
+                raise ValueError("10x h5 has no features group")
+            adata = AnnData(
+                matrix,
+                obs=obs_dict,
+                var=var_dict,
+            )
+            logg.info("", time=start)
+            return adata
+        except KeyError:
+            raise Exception("File is missing one or more required datasets.")
+
+
+def read_visium(
+    path: Path | str,
+    genome: str | None = None,
+    *,
+    count_file: str = "filtered_feature_bc_matrix.h5",
+    library_id: str | None = None,
+    load_images: bool | None = True,
+    source_image_path: Path | str | None = None,
+) -> AnnData:
+    """\
+    Read 10x-Genomics-formatted visum dataset.
+
+    In addition to reading regular 10x output,
+    this looks for the `spatial` folder and loads images,
+    coordinates and scale factors.
+    Based on the `Space Ranger output docs`_.
+
+    See :func:`~scanpy.pl.spatial` for a compatible plotting function.
+
+    .. _Space Ranger output docs: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/output/overview
+
+    Parameters
+    ----------
+    path
+        Path to directory for visium datafiles.
+    genome
+        Filter expression to genes within this genome.
+    count_file
+        Which file in the passed directory to use as the count file. Typically would be one of:
+        'filtered_feature_bc_matrix.h5' or 'raw_feature_bc_matrix.h5'.
+    library_id
+        Identifier for the visium library. Can be modified when concatenating multiple adata objects.
+    source_image_path
+        Path to the high-resolution tissue image. Path will be included in
+        `.uns["spatial"][library_id]["metadata"]["source_image_path"]`.
+
+    Returns
+    -------
+    Annotated data matrix, where observations/cells are named by their
+    barcode and variables/genes by gene name. Stores the following information:
+
+    :attr:`~anndata.AnnData.X`
+        The data matrix is stored
+    :attr:`~anndata.AnnData.obs_names`
+        Cell names
+    :attr:`~anndata.AnnData.var_names`
+        Gene names for a feature barcode matrix, probe names for a probe bc matrix
+    :attr:`~anndata.AnnData.var`\\ `['gene_ids']`
+        Gene IDs
+    :attr:`~anndata.AnnData.var`\\ `['feature_types']`
+        Feature types
+    :attr:`~anndata.AnnData.obs`\\ `[filtered_barcodes]`
+        filtered barcodes if present in the matrix
+    :attr:`~anndata.AnnData.var`
+        Any additional metadata present in /matrix/features is read in.
+    :attr:`~anndata.AnnData.uns`\\ `['spatial']`
+        Dict of spaceranger output files with 'library_id' as key
+    :attr:`~anndata.AnnData.uns`\\ `['spatial'][library_id]['images']`
+        Dict of images (`'hires'` and `'lowres'`)
+    :attr:`~anndata.AnnData.uns`\\ `['spatial'][library_id]['scalefactors']`
+        Scale factors for the spots
+    :attr:`~anndata.AnnData.uns`\\ `['spatial'][library_id]['metadata']`
+        Files metadata: 'chemistry_description', 'software_version', 'source_image_path'
+    :attr:`~anndata.AnnData.obsm`\\ `['spatial']`
+        Spatial spot coordinates, usable as `basis` by :func:`~scanpy.pl.embedding`.
+    """
+    path = Path(path)
+    adata = read_10x_h5(path / count_file, genome=genome)
+
+    adata.uns["spatial"] = dict()
+
+    from h5py import File
+
+    with File(path / count_file, mode="r") as f:
+        attrs = dict(f.attrs)
+    if library_id is None:
+        library_id = str(attrs.pop("library_ids")[0], "utf-8")
+
+    adata.uns["spatial"][library_id] = dict()
+
+    if load_images:
+        tissue_positions_file = (
+            path / "spatial/tissue_positions.csv"
+            if (path / "spatial/tissue_positions.csv").exists()
+            else path / "spatial/tissue_positions_list.csv"
+        )
+        files = dict(
+            tissue_positions_file=tissue_positions_file,
+            scalefactors_json_file=path / "spatial/scalefactors_json.json",
+            hires_image=path / "spatial/tissue_hires_image.png",
+            lowres_image=path / "spatial/tissue_lowres_image.png",
+        )
+
+        # check if files exists, continue if images are missing
+        for f in files.values():
+            if not f.exists():
+                if any(x in str(f) for x in ["hires_image", "lowres_image"]):
+                    logg.warning(
+                        f"You seem to be missing an image file.\nCould not find '{f}'."
+                    )
+                else:
+                    raise OSError(f"Could not find '{f}'")
+
+        adata.uns["spatial"][library_id]["images"] = dict()
+        for res in ["hires", "lowres"]:
+            try:
+                adata.uns["spatial"][library_id]["images"][res] = imread(
+                    str(files[f"{res}_image"])
+                )
+            except Exception:
+                raise OSError(f"Could not find '{res}_image'")
+
+        # read json scalefactors
+        adata.uns["spatial"][library_id]["scalefactors"] = json.loads(
+            files["scalefactors_json_file"].read_bytes()
+        )
+
+        adata.uns["spatial"][library_id]["metadata"] = {
+            k: (str(attrs[k], "utf-8") if isinstance(attrs[k], bytes) else attrs[k])
+            for k in ("chemistry_description", "software_version")
+            if k in attrs
+        }
+
+        # read coordinates
+        positions = pd.read_csv(
+            files["tissue_positions_file"],
+            header=0 if tissue_positions_file.name == "tissue_positions.csv" else None,
+            index_col=0,
+        )
+        positions.columns = [
+            "in_tissue",
+            "array_row",
+            "array_col",
+            "pxl_col_in_fullres",
+            "pxl_row_in_fullres",
+        ]
+
+        adata.obs = adata.obs.join(positions, how="left")
+
+        adata.obsm["spatial"] = adata.obs[
+            ["pxl_row_in_fullres", "pxl_col_in_fullres"]
+        ].to_numpy()
+        adata.obs.drop(
+            columns=["pxl_row_in_fullres", "pxl_col_in_fullres"],
+            inplace=True,
+        )
+
+        # put image path in uns
+        if source_image_path is not None:
+            # get an absolute path
+            source_image_path = str(Path(source_image_path).resolve())
+            adata.uns["spatial"][library_id]["metadata"]["source_image_path"] = str(
+                source_image_path
+            )
+
+    return adata
+
+
+@old_positionals("var_names", "make_unique", "cache", "cache_compression", "gex_only")
+def read_10x_mtx(
+    path: Path | str,
+    *,
+    var_names: Literal["gene_symbols", "gene_ids"] = "gene_symbols",
+    make_unique: bool = True,
+    cache: bool = False,
+    cache_compression: Literal["gzip", "lzf"] | None | Empty = _empty,
+    gex_only: bool = True,
+    prefix: str | None = None,
+) -> AnnData:
+    """\
+    Read 10x-Genomics-formatted mtx directory.
+
+    Parameters
+    ----------
+    path
+        Path to directory for `.mtx` and `.tsv` files,
+        e.g. './filtered_gene_bc_matrices/hg19/'.
+    var_names
+        The variables index.
+    make_unique
+        Whether to make the variables index unique by appending '-1',
+        '-2' etc. or not.
+    cache
+        If `False`, read from source, if `True`, read from fast 'h5ad' cache.
+    cache_compression
+        See the h5py :ref:`dataset_compression`.
+        (Default: `settings.cache_compression`)
+    gex_only
+        Only keep 'Gene Expression' data and ignore other feature types,
+        e.g. 'Antibody Capture', 'CRISPR Guide Capture', or 'Custom'
+    prefix
+        Any prefix before `matrix.mtx`, `genes.tsv` and `barcodes.tsv`. For instance,
+        if the files are named `patientA_matrix.mtx`, `patientA_genes.tsv` and
+        `patientA_barcodes.tsv` the prefix is `patientA_`.
+        (Default: no prefix)
+
+    Returns
+    -------
+    An :class:`~anndata.AnnData` object
+    """
+    path = Path(path)
+    prefix = "" if prefix is None else prefix
+    is_legacy = (path / f"{prefix}genes.tsv").is_file()
+    adata = _read_10x_mtx(
+        path,
+        var_names=var_names,
+        make_unique=make_unique,
+        cache=cache,
+        cache_compression=cache_compression,
+        prefix=prefix,
+        is_legacy=is_legacy,
+    )
+    if is_legacy or not gex_only:
+        return adata
+    gex_rows = adata.var["feature_types"] == "Gene Expression"
+    return adata[:, gex_rows].copy()
+
+
+def _read_10x_mtx(
+    path: Path,
+    *,
+    var_names: Literal["gene_symbols", "gene_ids"] = "gene_symbols",
+    make_unique: bool = True,
+    cache: bool = False,
+    cache_compression: Literal["gzip", "lzf"] | None | Empty = _empty,
+    prefix: str = "",
+    is_legacy: bool,
+) -> AnnData:
+    """
+    Read mex from output from Cell Ranger v2- or v3+
+    """
+    suffix = "" if is_legacy else ".gz"
+    adata = read(
+        path / f"{prefix}matrix.mtx{suffix}",
+        cache=cache,
+        cache_compression=cache_compression,
+    ).T  # transpose the data
+    genes = pd.read_csv(
+        path / f"{prefix}{'genes' if is_legacy else 'features'}.tsv{suffix}",
+        header=None,
+        sep="\t",
+    )
+    if var_names == "gene_symbols":
+        var_names_idx = pd.Index(genes[1].values)
+        if make_unique:
+            var_names_idx = anndata.utils.make_index_unique(var_names_idx)
+        adata.var_names = var_names_idx
+        adata.var["gene_ids"] = genes[0].values
+    elif var_names == "gene_ids":
+        adata.var_names = genes[0].values
+        adata.var["gene_symbols"] = genes[1].values
+    else:
+        raise ValueError("`var_names` needs to be 'gene_symbols' or 'gene_ids'")
+    if not is_legacy:
+        adata.var["feature_types"] = genes[2].values
+    barcodes = pd.read_csv(path / f"{prefix}barcodes.tsv{suffix}", header=None)
+    adata.obs_names = barcodes[0].values
+    return adata
+
+
+@old_positionals("ext", "compression", "compression_opts")
+def write(
+    filename: Path | str,
+    adata: AnnData,
+    *,
+    ext: Literal["h5", "csv", "txt", "npz"] | None = None,
+    compression: Literal["gzip", "lzf"] | None = "gzip",
+    compression_opts: int | None = None,
+):
+    """\
+    Write :class:`~anndata.AnnData` objects to file.
+
+    Parameters
+    ----------
+    filename
+        If the filename has no file extension, it is interpreted as a key for
+        generating a filename via `sc.settings.writedir / (filename +
+        sc.settings.file_format_data)`. This is the same behavior as in
+        :func:`~scanpy.read`.
+    adata
+        Annotated data matrix.
+    ext
+        File extension from wich to infer file format. If `None`, defaults to
+        `sc.settings.file_format_data`.
+    compression
+        See https://docs.h5py.org/en/latest/high/dataset.html.
+    compression_opts
+        See https://docs.h5py.org/en/latest/high/dataset.html.
+    """
+    filename = Path(filename)  # allow passing strings
+    if is_valid_filename(filename):
+        filename = filename
+        ext_ = is_valid_filename(filename, return_ext=True)
+        if ext is None:
+            ext = ext_
+        elif ext != ext_:
+            raise ValueError(
+                "It suffices to provide the file type by "
+                "providing a proper extension to the filename."
+                'One of "txt", "csv", "h5" or "npz".'
+            )
+    else:
+        key = filename
+        ext = settings.file_format_data if ext is None else ext
+        filename = _get_filename_from_key(key, ext)
+    if ext == "csv":
+        adata.write_csvs(filename)
+    else:
+        adata.write(
+            filename, compression=compression, compression_opts=compression_opts
+        )
+
+
+# -------------------------------------------------------------------------------
+# Reading and writing parameter files
+# -------------------------------------------------------------------------------
+
+
+@old_positionals("as_header")
+def read_params(
+    filename: Path | str, *, as_header: bool = False
+) -> dict[str, int | float | bool | str | None]:
+    """\
+    Read parameter dictionary from text file.
+
+    Assumes that parameters are specified in the format::
+
+        par1 = value1
+        par2 = value2
+
+    Comments that start with '#' are allowed.
+
+    Parameters
+    ----------
+    filename
+        Filename of data file.
+    asheader
+        Read the dictionary from the header (comment section) of a file.
+
+    Returns
+    -------
+    Dictionary that stores parameters.
+    """
+    filename = Path(filename)  # allow passing str objects
+    from collections import OrderedDict
+
+    params = OrderedDict([])
+    for line in filename.open():
+        if "=" in line and (not as_header or line.startswith("#")):
+            line = line[1:] if line.startswith("#") else line
+            key, val = line.split("=")
+            key = key.strip()
+            val = val.strip()
+            params[key] = convert_string(val)
+    return params
+
+
+def write_params(path: Path | str, *args, **maps):
+    """\
+    Write parameters to file, so that it's readable by read_params.
+
+    Uses INI file format.
+    """
+    path = Path(path)
+    if not path.parent.is_dir():
+        path.parent.mkdir(parents=True)
+    if len(args) == 1:
+        maps[None] = args[0]
+    with path.open("w") as f:
+        for header, map in maps.items():
+            if header is not None:
+                f.write(f"[{header}]\n")
+            for key, val in map.items():
+                f.write(f"{key} = {val}\n")
+
+
+# -------------------------------------------------------------------------------
+# Reading and Writing data files
+# -------------------------------------------------------------------------------
+
+
+def _read(
+    filename: Path,
+    *,
+    backed=None,
+    sheet=None,
+    ext=None,
+    delimiter=None,
+    first_column_names=None,
+    backup_url=None,
+    cache=False,
+    cache_compression=None,
+    suppress_cache_warning=False,
+    **kwargs,
+):
+    if ext is not None and ext not in avail_exts:
+        raise ValueError(
+            f"Please provide one of the available extensions.\n{avail_exts}"
+        )
+    else:
+        ext = is_valid_filename(filename, return_ext=True)
+    is_present = _check_datafile_present_and_download(filename, backup_url=backup_url)
+    if not is_present:
+        logg.debug(f"... did not find original file {filename}")
+    # read hdf5 files
+    if ext in {"h5", "h5ad"}:
+        if sheet is None:
+            return read_h5ad(filename, backed=backed)
+        else:
+            logg.debug(f"reading sheet {sheet} from file {filename}")
+            return read_hdf(filename, sheet)
+    # read other file types
+    path_cache: Path = settings.cachedir / _slugify(filename).replace(
+        f".{ext}", ".h5ad"
+    )
+    if path_cache.suffix in {".gz", ".bz2"}:
+        path_cache = path_cache.with_suffix("")
+    if cache and path_cache.is_file():
+        logg.info(f"... reading from cache file {path_cache}")
+        return read_h5ad(path_cache)
+
+    if not is_present:
+        raise FileNotFoundError(f"Did not find file {filename}.")
+    logg.debug(f"reading {filename}")
+    if not cache and not suppress_cache_warning:
+        logg.hint(
+            "This might be very slow. Consider passing `cache=True`, "
+            "which enables much faster reading from a cache file."
+        )
+    # do the actual reading
+    if ext == "xlsx" or ext == "xls":
+        if sheet is None:
+            raise ValueError("Provide `sheet` parameter when reading '.xlsx' files.")
+        else:
+            adata = read_excel(filename, sheet)
+    elif ext in {"mtx", "mtx.gz"}:
+        adata = read_mtx(filename)
+    elif ext == "csv":
+        if delimiter is None:
+            delimiter = ","
+        adata = read_csv(
+            filename, first_column_names=first_column_names, delimiter=delimiter
+        )
+    elif ext in {"txt", "tab", "data", "tsv"}:
+        if ext == "data":
+            logg.hint(
+                "... assuming '.data' means tab or white-space separated text file",
+            )
+            logg.hint("change this by passing `ext` to sc.read")
+        adata = read_text(filename, delimiter, first_column_names)
+    elif ext == "soft.gz":
+        adata = _read_softgz(filename)
+    elif ext == "loom":
+        adata = read_loom(filename=filename, **kwargs)
+    else:
+        raise ValueError(f"Unknown extension {ext}.")
+    if cache:
+        logg.info(
+            f"... writing an {settings.file_format_data} "
+            "cache file to speedup reading next time"
+        )
+        if cache_compression is _empty:
+            cache_compression = settings.cache_compression
+        if not path_cache.parent.is_dir():
+            path_cache.parent.mkdir(parents=True)
+        # write for faster reading when calling the next time
+        adata.write(path_cache, compression=cache_compression)
+    return adata
+
+
+def _slugify(path: str | PurePath) -> str:
+    """Make a path into a filename."""
+    if not isinstance(path, PurePath):
+        path = PurePath(path)
+    parts = list(path.parts)
+    if parts[0] == "/":
+        parts.pop(0)
+    elif len(parts[0]) == 3 and parts[0][1:] == ":\\":
+        parts[0] = parts[0][0]  # C:\ → C
+    filename = "-".join(parts)
+    assert "/" not in filename, filename
+    assert not filename[1:].startswith(":"), filename
+    return filename
+
+
+def _read_softgz(filename: str | bytes | Path | BinaryIO) -> AnnData:
+    """\
+    Read a SOFT format data file.
+
+    The SOFT format is documented here
+    https://www.ncbi.nlm.nih.gov/geo/info/soft.html.
+
+    Notes
+    -----
+    The function is based on a script by Kerby Shedden.
+    https://dept.stat.lsa.umich.edu/~kshedden/Python-Workshop/gene_expression_comparison.html
+    """
+    import gzip
+
+    with gzip.open(filename, mode="rt") as file:
+        # The header part of the file contains information about the
+        # samples. Read that information first.
+        samples_info = {}
+        for line in file:
+            if line.startswith("!dataset_table_begin"):
+                break
+            elif line.startswith("!subset_description"):
+                subset_description = line.split("=")[1].strip()
+            elif line.startswith("!subset_sample_id"):
+                subset_ids = line.split("=")[1].split(",")
+                subset_ids = [x.strip() for x in subset_ids]
+                for k in subset_ids:
+                    samples_info[k] = subset_description
+        # Next line is the column headers (sample id's)
+        sample_names = file.readline().strip().split("\t")
+        # The column indices that contain gene expression data
+        indices = [i for i, x in enumerate(sample_names) if x.startswith("GSM")]
+        # Restrict the column headers to those that we keep
+        sample_names = [sample_names[i] for i in indices]
+        # Get a list of sample labels
+        groups = [samples_info[k] for k in sample_names]
+        # Read the gene expression data as a list of lists, also get the gene
+        # identifiers
+        gene_names, X = [], []
+        for line in file:
+            # This is what signals the end of the gene expression data
+            # section in the file
+            if line.startswith("!dataset_table_end"):
+                break
+            V = line.split("\t")
+            # Extract the values that correspond to gene expression measures
+            # and convert the strings to numbers
+            x = [float(V[i]) for i in indices]
+            X.append(x)
+            gene_names.append(V[1])
+    # Convert the Python list of lists to a Numpy array and transpose to match
+    # the Scanpy convention of storing samples in rows and variables in colums.
+    X = np.array(X).T
+    obs = pd.DataFrame({"groups": groups}, index=sample_names)
+    var = pd.DataFrame(index=gene_names)
+    return AnnData(X=X, obs=obs, var=var)
+
+
+# -------------------------------------------------------------------------------
+# Type conversion
+# -------------------------------------------------------------------------------
+
+
+def is_float(string: str) -> float:
+    """Check whether string is float.
+
+    See also
+    --------
+    https://stackoverflow.com/questions/736043/checking-if-a-string-can-be-converted-to-float-in-python
+    """
+    try:
+        float(string)
+        return True
+    except ValueError:
+        return False
+
+
+def is_int(string: str) -> bool:
+    """Check whether string is integer."""
+    try:
+        int(string)
+        return True
+    except ValueError:
+        return False
+
+
+def convert_bool(string: str) -> tuple[bool, bool]:
+    """Check whether string is boolean."""
+    if string == "True":
+        return True, True
+    elif string == "False":
+        return True, False
+    else:
+        return False, False
+
+
+def convert_string(string: str) -> int | float | bool | str | None:
+    """Convert string to int, float or bool."""
+    if is_int(string):
+        return int(string)
+    elif is_float(string):
+        return float(string)
+    elif convert_bool(string)[0]:
+        return convert_bool(string)[1]
+    elif string == "None":
+        return None
+    else:
+        return string
+
+
+# -------------------------------------------------------------------------------
+# Helper functions for reading and writing
+# -------------------------------------------------------------------------------
+
+
+def get_used_files():
+    """Get files used by processes with name scanpy."""
+    import psutil
+
+    loop_over_scanpy_processes = (
+        proc for proc in psutil.process_iter() if proc.name() == "scanpy"
+    )
+    filenames = []
+    for proc in loop_over_scanpy_processes:
+        try:
+            flist = proc.open_files()
+            for nt in flist:
+                filenames.append(nt.path)
+        # This catches a race condition where a process ends
+        # before we can examine its files
+        except psutil.NoSuchProcess:
+            pass
+    return set(filenames)
+
+
+def _get_filename_from_key(key, ext=None) -> Path:
+    ext = settings.file_format_data if ext is None else ext
+    return settings.writedir / f"{key}.{ext}"
+
+
+def _download(url: str, path: Path):
+    try:
+        import ipywidgets  # noqa: F401
+        from tqdm.auto import tqdm
+    except ImportError:
+        from tqdm import tqdm
+
+    from urllib.error import URLError
+    from urllib.request import Request, urlopen
+
+    blocksize = 1024 * 8
+    blocknum = 0
+
+    try:
+        req = Request(url, headers={"User-agent": "scanpy-user"})
+
+        try:
+            open_url = urlopen(req)
+        except URLError:
+            logg.warning(
+                "Failed to open the url with default certificates, trying with certifi."
+            )
+
+            from ssl import create_default_context
+
+            from certifi import where
+
+            open_url = urlopen(req, context=create_default_context(cafile=where()))
+
+        with open_url as resp:
+            total = resp.info().get("content-length", None)
+            with (
+                tqdm(
+                    unit="B",
+                    unit_scale=True,
+                    miniters=1,
+                    unit_divisor=1024,
+                    total=total if total is None else int(total),
+                ) as t,
+                path.open("wb") as f,
+            ):
+                block = resp.read(blocksize)
+                while block:
+                    f.write(block)
+                    blocknum += 1
+                    t.update(len(block))
+                    block = resp.read(blocksize)
+
+    except (KeyboardInterrupt, Exception):
+        # Make sure file doesn’t exist half-downloaded
+        if path.is_file():
+            path.unlink()
+        raise
+
+
+def _check_datafile_present_and_download(path, backup_url=None):
+    """Check whether the file is present, otherwise download."""
+    path = Path(path)
+    if path.is_file():
+        return True
+    if backup_url is None:
+        return False
+    logg.info(
+        f"try downloading from url\n{backup_url}\n"
+        "... this may take a while but only happens once"
+    )
+    if not path.parent.is_dir():
+        logg.info(f"creating directory {path.parent}/ for saving data")
+        path.parent.mkdir(parents=True)
+
+    _download(backup_url, path)
+    return True
+
+
+def is_valid_filename(filename: Path, *, return_ext: bool = False):
+    """Check whether the argument is a filename."""
+    ext = filename.suffixes
+
+    if len(ext) > 2:
+        logg.warning(
+            f"Your filename has more than two extensions: {ext}.\n"
+            f"Only considering the two last: {ext[-2:]}."
+        )
+        ext = ext[-2:]
+
+    # cases for gzipped/bzipped text files
+    if len(ext) == 2 and ext[0][1:] in text_exts and ext[1][1:] in ("gz", "bz2"):
+        return ext[0][1:] if return_ext else True
+    elif ext and ext[-1][1:] in avail_exts:
+        return ext[-1][1:] if return_ext else True
+    elif "".join(ext) == ".soft.gz":
+        return "soft.gz" if return_ext else True
+    elif "".join(ext) == ".mtx.gz":
+        return "mtx.gz" if return_ext else True
+    elif not return_ext:
+        return False
+    raise ValueError(
+        f"""\
+{filename!r} does not end on a valid extension.
+Please, provide one of the available extensions.
+{avail_exts}
+Text files with .gz and .bz2 extensions are also supported.\
+"""
+    )