metacell.dynamake package

Submodules

metacell.dynamake.analysis module

Build steps for analyzing metacell data.

metacell.dynamake.common module

Common functions for DynaMake steps.

async metacell.dynamake.common.call(name: Optional[str] = None, *, with_config: bool = False, with_parallel: bool = False, with_intermediate: bool = False, log_context: Optional[str] = None, **kwargs) → None

Invoke the metacell_call script to invoke some top-level Python function.

If the called function name is not specified, it is assumed to be identical to the current step name.

If with_config is True, then a --config parameter is added using dynamake.application.with_config().

If with_parallel is True, then --jobs is added with a value computed by :py:func:tgutils.make.parallel_jobs, that is, taking into account the innermost :py:func:tgutils.make.tg_require.

If with_intermediate is True, then the program uses the write_intermediate parameter.

The first named argument is special; it is automatically emphasized, and also passed to the --log_context command line option. You can disable this by providing an explicit log_context (which may be empty).

async metacell.dynamake.common.ecall(name: Optional[str] = None, *, with_config: bool = False, with_parallel: bool = False, with_intermediate: bool = False, log_context: Optional[str] = None, **kwargs) → None

Similar to call but first e-xpand all the named arguments.

metacell.dynamake.common.erequire_ancestor(nested_path: str) → str

Require a file which may exist in a parent directory.

Searches for the file in the nested directory, and failing that, in its parent(s), up to and including the current directory (but no further).

metacell.dynamake.group module

[:,np.newaxis] Build steps for grouping cells to metacells.

async metacell.dynamake.group.group_few_profiles(profiles_dir: str) → None

async metacell.dynamake.group.group_many_profiles(profiles_dir: str) → None

metacell.dynamake.importation module

Build steps for importing raw data into the metacell pipeline.

async metacell.dynamake.importation.convert_10x() → None

async metacell.dynamake.importation.convert_hca() → None

async metacell.dynamake.importation.convert_moca() → None

metacell.dynamake.importation.standard_format_file(name: str) → str

metacell.dynamake.view module

Build steps for creating views of the data to analyze.

Module contents

DynaMake rules for the metacell work flow.