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>¶