PoolParty Documentation

PoolParty is a Python package that streamlines the design of complex DNA sequence libraries. Each library is specified as a computational graph in a few lines of code, with sequences generated on demand. Over 50 built-in operations cover nucleotide- and codon-level mutagenesis, scanning, barcode generation, and more. Applications include massively parallel reporter assays, deep mutational scanning, and in silico analysis of genomic models.

PoolParty overview: Pools represent sequence collections, Operations transform them, and together they form a directed acyclic graph (DAG) specifying the library design.

Why PoolParty?

Designing DNA libraries often involves combining multiple types of sequence modifications (mutations, insertions, deletions, replacements) across multiple regions. PoolParty lets you:

  • Chain operations: Build pipelines from operations like mutagenize, deletion_scan, and insertion_scan to produce complex variant libraries

  • Tag regions: Mark segments of a sequence with XML-style tags so operations can target them by name

  • Track construction history: Each sequence carries a design card recording how it was built, ready for filtering and analysis

  • Style output: Visual annotations highlight mutations, deletions, and regions for quick auditing

PoolParty provides over 50 built-in operations across six categories. See Operations for the full catalog.

Installation

Install from PyPI:

pip install poolparty

Or install from source:

git clone https://github.com/jbkinney/poolparty-statetracker.git
cd poolparty-statetracker/poolparty
pip install -e .

Example

Stack different variant types into a single barcoded library:

import poolparty as pp

pp.init()

template = pp.from_seq("ACGT<cre>GGAAAGCGGGCAGTGAGC</cre>TTTT<bc/>GGGG")

mutations = template.mutagenize(region="cre", num_mutations=1)
deletions = template.deletion_scan(region="cre", deletion_length=5)

combined = pp.stack([mutations, deletions])
library = combined.insert_kmers(region="bc", length=10).named("library")

library.print_library(num_seqs=6, seed=0)
library: seq_length=40, num_states=2 ACGT<cre>GGAAAGCGGCCAGTGAGC</cre>TTTT<bc>CCGATGGGGG</bc>GGGG
ACGT<cre>GGAAAGCGGGCAG-----</cre>TTTT<bc>TTCGGGATAG</bc>GGGG
ACGT<cre>GGAAAGCGGACAGTGAGC</cre>TTTT<bc>TACCTATTTT</bc>GGGG
ACGT<cre>GGA-----GGCAGTGAGC</cre>TTTT<bc>CTTGAATGGC</bc>GGGG
ACGT<cre>GGAGAGCGGGCAGTGAGC</cre>TTTT<bc>CGCAGCCTGG</bc>GGGG
ACGT<cre>GGAAAG-----AGTGAGC</cre>TTTT<bc>AACTGGTCGG</bc>GGGG

The Quickstart Guide walks through each concept step by step. For complete real-world examples, see the Tutorials.

Contents

User Guide

Reference

Indices and Tables

See Also

  • StateTracker: Composable states for combinatorial enumeration (used internally by PoolParty)