capellini.stages.network

Network stage: build common-abundance, shrinkage, CRISPR, smoothed, and X* outputs.

Functions

`build_common_abundance_one`(study, cfg)	Build the aligned, prevalence-filtered common abundance tables.
`build_raw_crispr_one`(study, cfg)	Aggregate phage-host predictions into a raw CRISPR network.
`build_shrinkage_one`(study, cfg)	Compute shrinkage correlations on the bacteria-virus joint matrix.
`build_smooth_crispr_one`(study, cfg)	Smooth the raw CRISPR matrix using bacteria/virus taxonomy kernels.
`build_xstar_one`(study, cfg)	Build the CLR-transformed message-passing X* outputs.
`run_network`(cfg)	Run the network stage according to the RUN_* flags on the config.

capellini.stages.network.build_common_abundance_one(study: str, cfg: CapelliniConfig) → dict[str, Path][source]

Build the aligned, prevalence-filtered common abundance tables.

Parameters:

Returns:

Mapping of artefact name to written file path.

capellini.stages.network.build_raw_crispr_one(study: str, cfg: CapelliniConfig) → Path[source]: Aggregate phage-host predictions into a raw CRISPR network.

capellini.stages.network.build_shrinkage_one(study: str, cfg: CapelliniConfig) → dict[str, Path][source]: Compute shrinkage correlations on the bacteria-virus joint matrix.

capellini.stages.network.build_smooth_crispr_one(study: str, cfg: CapelliniConfig) → dict[str, Path][source]: Smooth the raw CRISPR matrix using bacteria/virus taxonomy kernels.

capellini.stages.network.build_xstar_one(study: str, cfg: CapelliniConfig) → dict[str, Path][source]: Build the CLR-transformed message-passing X* outputs.

capellini.stages.network.run_network(cfg: CapelliniConfig) → dict[str, dict][source]

Run the network stage according to the RUN_* flags on the config.