How to use the anndata.read_csv function in anndata

To help you get started, we’ve selected a few anndata examples, based on popular ways it is used in public projects.

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github theislab / scanpy / scanpy / readwrite.py View on Github external
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':
        adata = read_csv(filename, first_column_names=first_column_names)
    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(