How to use the anndata.read_h5ad function in anndata

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github gao-lab / Cell_BLAST / test / test_data.py View on Github external
def test_anndata(self):
        ad = self.ds.to_anndata()
        ad.write_h5ad("./test.h5ad")
        ds = cb.data.ExprDataSet.from_anndata(anndata.read_h5ad("./test.h5ad"))
        self._compare_datasets(self.ds, ds)
github YosefLab / scVI / scvi / inference / posterior_utils.py View on Github external
with open(post_type_path, "r") as post_file:
        post_class_str = post_file.readline()
    str_to_classes = dict(
        TotalPosterior=TotalPosterior,
        JPosterior=JPosterior,
        Posterior=Posterior,
        AnnotationPosterior=AnnotationPosterior,
    )
    if post_class_str not in str_to_classes:
        raise ValueError(
            "Posterior type {} not eligible for loading".format(post_class_str)
        )
    post_class = str_to_classes[post_class_str]

    # Loading dataset and associated measurements
    ad = anndata.read_h5ad(filename=dataset_path)
    key = "cell_measurements_col_mappings"
    if key in ad.uns:
        cell_measurements_col_mappings = ad.uns[key]
    else:
        cell_measurements_col_mappings = dict()
    dataset = AnnDatasetFromAnnData(
        ad=ad, cell_measurements_col_mappings=cell_measurements_col_mappings
    )

    # Loading scVI model
    if use_cuda == "auto":
        use_cuda = torch.cuda.is_available()
    use_cuda = use_cuda and torch.cuda.is_available()
    if use_cuda:
        model.load_state_dict(torch.load(model_path))
        model.cuda()
github normjam / benchmark / normbench / methods / data.py View on Github external
def _download_adata(url) -> AnnData:
    response = requests.get(url)
    f = BytesIO(response.content)
    return read_h5ad(f)
github chanzuckerberg / cellxgene / server / app / scanpy_engine / scanpy_engine.py View on Github external
def _load_data(self, data_locator):
        # as of AnnData 0.6.19, backed mode performs initial load fast, but at the
        # cost of significantly slower access to X data.
        try:
            # there is no guarantee data_locator indicates a local file.  The AnnData
            # API will only consume local file objects.  If we get a non-local object,
            # make a copy in tmp, and delete it after we load into memory.
            with data_locator.local_handle() as lh:
                # as of AnnData 0.6.19, backed mode performs initial load fast, but at the
                # cost of significantly slower access to X data.
                backed = 'r' if self.config['backed'] else None
                self.data = anndata.read_h5ad(lh, backed=backed)

        except ValueError:
            raise ScanpyFileError(
                "File must be in the .h5ad format. Please read "
                "https://github.com/theislab/scanpy_usage/blob/master/170505_seurat/info_h5ad.md to "
                "learn more about this format. You may be able to convert your file into this format "
                "using `cellxgene prepare`, please run `cellxgene prepare --help` for more "
                "information."
            )
        except MemoryError:
            raise ScanpyFileError("Out of memory - file is too large for available memory.")
        except Exception as e:
            raise ScanpyFileError(
                f"{e} - file not found or is inaccessible.  File must be an .h5ad object.  "
                f"Please check your input and try again."
github YosefLab / scVI / scvi / dataset / anndataset.py View on Github external
def populate(self):
        ad = anndata.read_h5ad(
            os.path.join(self.save_path, self.filenames[0])
        )  # obs = cells, var = genes

        # extract GeneExpressionDataset relevant attributes
        # and provide access to annotations from the underlying AnnData object.
        (
            X,
            batch_indices,
            labels,
            gene_names,
            cell_types,
            obs,
            obsm,
            var,
            _,
            uns,