combine (function)

Combine the content of several Loom files

loompy.combine(files: List[str], output_file: str, key: str = None, file_attrs: Dict[str, str] = None, batch_size: int = 1000, convert_attrs: bool = False) → None[source]

Combine two or more loom files and save as a new loom file

Parameters:
  • files (list of str) – the list of input files (full paths)
  • output_file (str) – full path of the output loom file
  • key (string) – Row attribute to use to verify row ordering
  • file_attrs (dict) – file attributes (title, description, url, etc.)
  • batch_size (int) – limits the batch or cols/rows read in memory (default: 1000)
  • convert_attrs (bool) – convert file attributes that differ between files into column attributes
Returns:

Nothing, but creates a new loom file combining the input files.

Note that the loom files must have exactly the same number of rows, and must have exactly the same column attributes. Named layers not present in the first file are discarded.

Warning

If you don’t give a key argument, the files will be combined without changing the ordering of rows or columns. Row attributes will be taken from the first file. Hence, if rows are not in the same order in all files, the result may be meaningless.

To guard against this issue, you are strongly advised to provide a key argument, which is used to sort files while merging. The key should be the name of a row atrribute that contains a unique value for each row. For example, to order rows by the attribute Accession:

import loompy
loompy.combine(files, key="Accession")