Commandline interface

sfaira

Create and manage sfaira dataloaders.

sfaira [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

-v, --verbose

Enable verbose output (print debug statements).

-l, --log-file <log_file>

Save a verbose log to a file.

annotate-dataloader

Annotates a dataloader.

sfaira annotate-dataloader [OPTIONS]

Options

--doi <doi>

Required The doi of the paper that the data loader refers to.

--path-data <path_data>

Absolute path of the location of the raw data directory.

--path-loader <path_loader>

Relative path from the current directory to the location of the data loader.

--schema <schema>

The curation schema to check meta data availability for.

cache-clear

Clears sfaira cache, including ontology and genome cache.

sfaira cache-clear [OPTIONS]

cache-reload

Downloads new ontology versions into cache.

sfaira cache-reload [OPTIONS]

create-dataloader

Interactively create a new sfaira dataloader.

sfaira create-dataloader [OPTIONS]

Options

--path-data <path_data>

Absolute path of the desired location of the raw data directory.

--path-loader <path_loader>

Relative path from the current directory to the desired location of the data loader.

export-h5ad

Creates a collection of streamlined h5ad object for a given DOI.

sfaira export-h5ad [OPTIONS]

Options

--doi <doi>

Required The doi of the paper that the data loader refers to.

--schema <schema>

Schema to streamline to, e.g. ‘cellxgene’

--path-out <path_out>

Absolute path of the location of the streamlined output h5ads.

--path-data <path_data>

Absolute path of the location of the raw data directory.

--path-loader <path_loader>

Relative path from the current directory to the location of the data loader.

--path-cache <path_cache>

The optional absolute path to cached data library maintained by sfaira. Using such a cache speeds up loading in sequential runs but is not necessary.

finalize-dataloader

Formats .tsvs and runs a full data loader test.

sfaira finalize-dataloader [OPTIONS]

Options

--doi <doi>

Required The doi of the paper that the data loader refers to.

--path-data <path_data>

Absolute path of the location of the raw data directory.

--path-loader <path_loader>

Relative path from the current directory to the location of the data loader.

--schema <schema>

The curation schema to check meta data availability for.

publish-dataloader

Interactively create a GitHub pull request for a newly created data loader. This only works when called in the sfaira CLI docker container. Runs a full data loader test before starting the pull request.

sfaira publish-dataloader [OPTIONS]

test-dataloader

Runs a full data loader test.

sfaira test-dataloader [OPTIONS]

Options

--doi <doi>

Required The doi of the paper that the data loader refers to.

--path-data <path_data>

Absolute path of the location of the raw data directory.

--path-loader <path_loader>

Relative path from the current directory to the location of the data loader.

--schema <schema>

The curation schema to check meta data availability for.

validate-dataloader

Verifies the dataloader against sfaira’s requirements.

sfaira validate-dataloader [OPTIONS]

Options

--doi <doi>

Required The doi of the paper that the data loader refers to.

--path-loader <path_loader>

Relative path from the current directory to the desired location of the data loader.

--schema <schema>

The curation schema to check meta data availability for.

validate-h5ad

Runs a component test on a streamlined h5ad object.

h5ad is the absolute path of the .h5ad file to test. schema is the schema type (“cellxgene”,) to test.

sfaira validate-h5ad [OPTIONS]

Options

--h5ad <h5ad>
--schema <schema>