polyform-lattice 0.1.2

Structured analysis of proteoform distributions on finite, bounded, k-graded modal lattices.

PolyForm

PolyForm is a Python package for structured analysis of proteoform distributions. It maps measured proteoform catalogues onto finite, bounded, k-graded modal lattices and computes structure-derived metrics including state identity, occupancy, grade spread, support topology, native clustering, principal occupied components, and statistical surprise.

Install

pip install polyform-lattice

The import name is polyform; the PyPI distribution name is polyform-lattice (the plain name polyform was already taken by an unrelated project). So you pip install polyform-lattice but import polyform.

From source (for development):

git clone https://github.com/JamesCobley/PolyForm.git
cd PolyForm
pip install -e .

Usage

Python API

Each analysis is a single call that returns a dict of pandas DataFrames and, by default, writes CSVs and figures to an output directory.

import polyform

# Global support-mode structural metrics on the choice-free modal lattice
support = polyform.run_support_mode(csv="proteoforms.csv", outdir="out_support")
support["global"]           # one-row global summary
support["protein_metrics"]  # protein-level structural metrics
support["grade"]            # protein-by-grade metrics

# Demonstration occupancy metrics on real observed supports
weight = polyform.run_weight_mode(csv="proteoforms.csv", outdir="out_weight")
weight["selected"]          # proteins selected for demonstration
weight["metrics"]           # occupancy-dependent metrics

# Tissue-resolved Hamming-1 support topology on a top-down atlas
topology = polyform.run_topology(xlsx="atlas.xlsx", outdir="out_topology")
topology["tissue_summary"]
topology["components"]

Set make_figures=False to skip figure rendering (faster; CSVs still written).

Command line

polyform support   --csv proteoforms.csv --outdir out_support
polyform weight    --csv proteoforms.csv --outdir out_weight
polyform topology  --xlsx atlas.xlsx     --outdir out_topology

polyform support --help      # per-command options
polyform --version

Core primitives

The lattice/topology/information primitives are importable directly:

from polyform.core import (
    parse_ptms, read_fasta, log10_comb, hamming_distance_state,
    connected_components_for_states, shannon_entropy, normalized_entropy,
)

Inputs

• Support / weight modes expect a proteoform catalogue CSV with at least Entry Accession and PTMs columns; protein lengths are resolved from an Isoform Sequence column or an optional --fasta. PTM strings use the RESID:<code>@<position> form, |-separated.
• Topology mode expects the multi-tissue top-down atlas spreadsheet (--sheet, default All_Tissues).

Outputs

Each mode writes a set of .csv tables plus publication .png/.pdf figures into its --outdir. See each function's docstring for the exact file list.

Reproducibility

The original manuscript analysis scripts are preserved unchanged under manuscript/ as the provenance record. The packaged run_* functions wrap those exact computational bodies (only parameterising configuration and routing outputs) and were validated to reproduce the manuscript reference outputs.

Releasing (maintainers)

Releases publish to PyPI via Trusted Publishing (OIDC — no API tokens). One-time setup: on PyPI, add a trusted publisher for the project pointing at this repo's publish.yml workflow and a pypi environment.

To cut a release:

# bump version in pyproject.toml and src/polyform/__init__.py, update CHANGELOG.md
git commit -am "Release v0.1.0"
git tag v0.1.0
git push origin main --tags

Pushing the tag triggers .github/workflows/publish.yml, which builds the sdist + wheel, runs twine check, and publishes to PyPI.

License

MIT © 2026 James N. Cobley