API reference

Top-level

capellini.config	Configuration dataclass for the CAPELLINI pipeline.
capellini.pipeline	Top-level pipeline orchestrator.

Stages

capellini.stages.preflight	Pre-flight stage: folder initialization and optional fresh-start cleanup.
capellini.stages.dada2	DADA2 stage: run DADA2_Pipe.R and move the generated FASTA.
capellini.stages.ncbi_mapping	NCBI mapping stage: download taxonomy names and assign real NCBI taxids.
capellini.stages.mmseqs2	MMSeqs2 stage: 16S reference, easy-search, and 3-layer NCBI/GCA assignment.
capellini.stages.spacepharer	SpacePHARER stage: spacer extraction, DB creation, prediction, and statistics.
capellini.stages.procs	ProCs stage: bacterial/viral protein extraction, clustering, and PA matrix.
capellini.stages.network	Network stage: common abundance, shrinkage, raw/smoothed CRISPR, residual X*.

Utilities

capellini.utils.io	I/O helpers: file reading, writing, downloading, subprocess execution.
capellini.utils.taxonomy	Taxonomy helpers: NCBI name lookup, index sanitization, bacteria taxonomy cleaning.
capellini.utils.transforms	Numerical transformations: CLR, row normalization, shrinkage correlation.
capellini.utils.network_utils	Network-level utilities: residual message passing, CRISPR smoothing, taxonomy kernels, abundance helpers.