Experiment

Experiment is GenAIRR's fluent pipeline builder. Every method returns the same Experiment extended by one pipeline stage; the pipeline runs when you call .run_records(...), .run(...), or .compile().run(...). For the conceptual walk-through - which methods are ancestor-phase vs descendant-phase, which clonal model to choose, how compile reuse works - see the Experiment builder guide. The reference below catalogues the public surface.

Common methods

The methods you'll reach for in most real pipelines:

Method	Purpose
.recombine(...)	Add the V(D)J recombination pass - the foundational ancestor-phase mechanism
.process_coding_ends(...)	Opt in to signed net processing of explicitly confirmed original coding ends
.productive_only()	Constrain sampling so only productive rearrangements survive
.mutate(...)	Apply biological SHM (uniform or S5F) on top of recombination
.clonal_lineage(...)	Grow BCR affinity-maturation lineage trees
.clonal_repertoire(...)	Generate TCR / flat-BCR abundance repertoires with clone sizes and duplicate_count
.expand_clones(...)	Legacy fixed-size clonal star model
.paired_end(...)	Project assembled sequences as paired R1 / R2 reads
.run_records(...)	Compile + run + return a SimulationResult

For the full pipeline-stage map (constraints, trim overrides, all the corruption methods, compile reuse, strict mode), see The Experiment builder.

Class reference

The autogenerated reference below comes straight from the docstrings in src/GenAIRR/experiment.py. This page is the pilot for the wider generated-reference effort.

GenAIRR.experiment.Experiment

Bases: _CorruptionMixin, _ConstraintsMixin, _ClonalMixin, _MutationMixin, _GenotypeAllelesMixin, _RecombinationMixin, _RefdataControlsMixin, _CompileMixin, _RunMixin, _IntrospectionMixin

Fluent builder for a simulation pipeline.

Build an Experiment from a config name, a :class:DataConfig, or a :class:GenAIRR._engine.RefDataConfig via :meth:Experiment.on, chain configuration steps (currently just :meth:recombine), then call :meth:run (or :meth:compile for explicit two-stage flow).

The builder is stateful but not destructive: each fluent call returns self after appending a step. The same Experiment can be compile()-d and run()-d multiple times with different seeds.

on(source) classmethod

Start an experiment against the given reference data.

source is one of: - a config-name string (e.g. "human_igh"), - a :class:GenAIRR.DataConfig instance, - a :class:GenAIRR._engine.RefDataConfig.

When source is a config name or a DataConfig, the underlying empirical distributions (NP lengths, per-gene trims) are kept on the experiment so :meth:recombine can use them as the default sampling distributions. A bare RefDataConfig has no such backing — :meth:recombine falls through to its uniform [0..6] placeholder unless the caller passes np1_lengths / np2_lengths explicitly.