Command-line entry points

Python entry points behind the rustscenic command. Handlers receive the argparse.Namespace assembled by main; use the command line for normal interactive use.

rustscenic.cli

rustscenic CLI entry point.

rustscenic grn --expression --tfs --output [--seed ...] rustscenic aucell --expression --regulons --output [--top-frac ...] rustscenic topics --expression --output [--n-topics --n-passes ...] rustscenic cistarget --rankings --regulons --output [--top-frac --auc-threshold] rustscenic --version

cmd_grn 

cmd_grn(args: Namespace) -> int

Run GRN inference for the grn command.

Parameters:

Name Type Description Default
args Namespace

Namespace parsed by main for the grn subcommand.

 required

Returns:

Type Description
int

Zero after writing the inferred edge table.

cmd_add_cor 

cmd_add_cor(args: Namespace) -> int

Add Pearson correlation and SCENIC polarity to GRN adjacencies.

Parameters:

Name Type Description Default
args Namespace

Namespace parsed by main for the add-cor subcommand.

 required

cmd_aucell 

cmd_aucell(args: Namespace) -> int

Score regulon activity for the aucell command.

Parameters:

Name Type Description Default
args Namespace

Namespace parsed by main for the aucell subcommand.

 required

Returns:

Type Description
int

Zero after writing activity scores and any requested metadata.

cmd_topics 

cmd_topics(args: Namespace) -> int

Fit a topic model for the topics command.

Parameters:

Name Type Description Default
args Namespace

Namespace parsed by main for the topics subcommand.

 required

Returns:

Type Description
int

Zero after writing the topic model outputs.

cmd_cistarget 

cmd_cistarget(args: Namespace) -> int

Score motif enrichment for the cistarget command.

Parameters:

Name Type Description Default
args Namespace

Namespace parsed by main for the cistarget subcommand.

 required

Returns:

Type Description
int

Zero after writing motif enrichment rows.

cmd_pipeline 

cmd_pipeline(args: Namespace) -> int

Run available stages through the public pipeline orchestrator.

Parameters:

Name Type Description Default
args Namespace

Namespace parsed by main for the pipeline subcommand.

 required

cmd_doctor 

cmd_doctor(args: Namespace) -> int

Check the installed Rust extension exposes all required symbols.

Parameters:

Name Type Description Default
args Namespace

Namespace parsed by main for the doctor subcommand.

 required

Returns:

Type Description
int

Zero if the backend check passes, otherwise one.

main 

main(argv: list[str] | None = None) -> int

Parse command-line arguments and dispatch the requested subcommand.

Parameters:

Name Type Description Default
argv list[str] | None

Arguments excluding the program name. None uses the process's command-line arguments, as in argparse.ArgumentParser.parse_args.

 None

Returns:

Type Description
int

Exit status returned by the selected command handler.