new (function)¶

Create a new empty Loom file and return it as a context manager.

loompy.new(filename: str, *, file_attrs: Optional[Dict[str, str]] = None) → loompy.loompy.LoomConnection[source]¶: Create an empty Loom file, and return it as a context manager.

The new() function is especially useful when you want to combine data from multiple sources. You would first create an empty Loom file, then add data to it incrementally. For example, using new() and scan():

with loompy.new(out_file) as dsout:  # Create a new, empty, loom file
  for f in input_files:  # Loop over a list of input Loom files
    with loompy.connect(f) as ds:
      totals = ds.map([np.sum], axis=1)[0]  # Calculate the total molecule count for each cell
      cells = np.where(totals > 500)[0] # Select the cells that passed QC (totals > 500)
      for (ix, selection, view) in ds.scan(items=cells, axis=1, key="Accession"):
        dsout.add_columns(view.layers, col_attrs=view.ca, row_attrs=view.ra)

Note the use of key=="Accession" which makes scan() sort the rows of each file by the row attribute Accession, ensuring that the resulting output is in a consistent order.