Operations
PoolParty provides composable operations for designing DNA sequence libraries.
Each operation returns a new Pool, so calls can be chained
into a declarative pipeline. All examples assume:
import poolparty as pp
pp.init()
Key concepts
Most operations accept a mode parameter that controls whether outputs are
enumerated exhaustively (sequential), sampled randomly (random), or
uniquely determined by the input (fixed). Each operation has internal
states determined by its mode and parameters — see Operation Modes for details.
When operations are combined, their internal states compose to determine the
output pool’s num_states — through multiplication, addition, or other rules
depending on the operation. See Library Size for details and a worked
example.
Every operation that accepts a pool argument is also available as a method
on any Pool. pp.mutagenize(wt, ...) and wt.mutagenize(...) are
equivalent, so operations can be chained left-to-right into a pipeline.
Source Operations
Create the initial Pools from which all downstream Pools are constructed. See Source Operations.
Transformation Operations
Modify sequence content through mutations, positional scanning, region manipulation, codon-level operations, and deterministic transforms.
Mutagenesis Operations — mutations, shuffling, recombination, and orientation flipping
Scanning Operations — systematic positional tiling (single and multi-window)
Region Operations — tag and manipulate named sequence regions
ORF Operations — codon-aware operations for protein-coding sequences
Sequence Utilities — deterministic per-sequence transforms
Composition Operations
Combine sequences from multiple Pools, either by concatenating sequences end-to-end or by merging state spaces. See Composition Operations.
State Operations
Control which sequences are in a Pool and how they are ordered, including methods to replicate, sample, filter, score, and synchronize. See State Operations.