CLI Modules

modalysis CLI entrypoint.

modalysis.main() → None[source]

Parse CLI args and dispatch to selected handler.

Return type:: None

Top-level CLI parser construction.

modalysis.cli.parsers.build_parser() → ArgumentParser[source]

Build and return the root argparse parser for modalysis CLI.

Return type:: ArgumentParser

CLI parser registration for server command.

modalysis.cli.parsers.server.register_server_parser(subparsers: _SubParsersAction) → None[source]

Register server command and arguments.

Parameters:: subparsers (_SubParsersAction)
Return type:: None

CLI parser registration for GFF command group.

modalysis.cli.parsers.gff.register_gff_parser(subparsers: _SubParsersAction) → None[source]

Register gff subcommands and arguments.

Parameters:: subparsers (_SubParsersAction)
Return type:: None

CLI parser registration for pileup command group.

modalysis.cli.parsers.pileup.register_pileup_parser(subparsers: _SubParsersAction) → None[source]

Register pileup subcommands and arguments.

Parameters:: subparsers (_SubParsersAction)
Return type:: None

CLI parser registration for DMR command group.

modalysis.cli.parsers.dmr.register_dmr_parser(subparsers: _SubParsersAction) → None[source]

Register dmr subcommands and arguments.

Parameters:: subparsers (_SubParsersAction)
Return type:: None

CLI parser registration for plot command group.

modalysis.cli.parsers.plot.register_plot_parser(subparsers: _SubParsersAction) → None[source]

Register plot subcommands and arguments.

Parameters:: subparsers (_SubParsersAction)
Return type:: None

CLI handler for starting the FastAPI server.

modalysis.cli.handlers.server.handle_server(args: Namespace) → None[source]

Handle modalysis server CLI command.

Parameters:: args (Namespace)
Return type:: None

CLI handlers for GFF commands.

modalysis.cli.handlers.gff.handle_gff_format(args: Namespace) → None[source]

Handle modalysis gff format CLI command.

Parameters:: args (Namespace)
Return type:: None

modalysis.cli.handlers.gff.handle_gff_annotate(args: Namespace) → None[source]

Handle modalysis gff annotate CLI command.

Parameters:: args (Namespace)
Return type:: None

CLI handlers for pileup commands.

modalysis.cli.handlers.pileup.handle_pileup_format(args: Namespace) → None[source]

Handle modalysis pileup format CLI command.

Parameters:: args (Namespace)
Return type:: None

modalysis.cli.handlers.pileup.handle_pileup_merge(args: Namespace) → None[source]

Handle modalysis pileup merge CLI command.

Parameters:: args (Namespace)
Return type:: None

CLI handlers for DMR commands.

modalysis.cli.handlers.dmr.handle_dmr_format(args: Namespace) → None[source]

Handle modalysis dmr format CLI command.

Parameters:: args (Namespace)
Return type:: None

modalysis.cli.handlers.dmr.handle_dmr_annotate(args: Namespace) → None[source]

Handle modalysis dmr annotate CLI command.

Parameters:: args (Namespace)
Return type:: None

modalysis.cli.handlers.dmr.handle_dmr_gene_counts(args: Namespace) → None[source]

Handle modalysis dmr gene-counts CLI command.

Parameters:: args (Namespace)
Return type:: None

modalysis.cli.handlers.dmr.handle_dmr_common_genes(args: Namespace) → None[source]

Handle modalysis dmr common-genes CLI command.

Parameters:: args (Namespace)
Return type:: None

CLI handlers for plot commands.

modalysis.cli.handlers.plot.handle_plot_mean_methylation(args: Namespace) → None[source]

Handle modalysis plot mean-methylation CLI command.

Parameters:: args (Namespace)
Return type:: None

modalysis.cli.handlers.plot.handle_plot_gene_heatmap(args: Namespace) → None[source]

Handle modalysis plot gene-heatmap CLI command.

Parameters:: args (Namespace)
Return type:: None

modalysis.cli.handlers.plot.handle_plot_dmr_dotplot(args: Namespace) → None[source]

Handle modalysis plot dmr-dotplot CLI command.

Parameters:: args (Namespace)
Return type:: None

modalysis.cli.handlers.plot.handle_plot_common_genes_venn(args: Namespace) → None[source]

Handle modalysis plot common-genes-venn CLI command.

Parameters:: args (Namespace)
Return type:: None