primer3plus-core 0.1.0

Headless Primer3Plus logic — Boulder-IO parsing, subprocess runners, no Flask dependency

primer3plus-core

Headless Python core for Primer3Plus — Boulder-IO parsing, subprocess runners, and settings management. No Flask dependency.

This package provides the non-Web logic extracted from the Primer3Plus server. It can be used as a standalone library to run Primer3 from Python without a browser.

Requirements

• Python >= 3.9
• primer3_core must be installed and available on PATH

Install

pip install primer3plus-core

Or from source:

git clone https://github.com/primer3-org/primer3plus-core.git
cd primer3plus-core
pip install .

Quick start

Prepare input and run Primer3

from primer3plus_core.boulder import prepare_input
from primer3plus_core.runner import run_primer3
from primer3plus_core.files import new_uuid, work_dir

# Prepare Boulder-IO input (normalises newlines, injects mispriming libs)
raw = open("my_input.txt").read()
prepared = prepare_input(raw)

# Write to a work directory
uuidstr = new_uuid()
sf = work_dir("data", uuidstr)
infile = f"{sf}/p3p_{uuidstr}_input.txt"
with open(infile, "w") as f:
    f.write(prepared)

# Run primer3_core
outfile = f"{sf}/p3p_{uuidstr}_output.txt"
error = run_primer3(infile, outfile,
                    f"{sf}/p3p_{uuidstr}_error.txt",
                    f"{sf}/p3p_{uuidstr}.log")
if error:
    print("Error:", error)
else:
    print(open(outfile).read())

Load default settings

from primer3plus_core.settings import load_default_settings

settings_json = load_default_settings()
print(settings_json[:80])

Parse prefold input (UNAFold)

from primer3plus_core.boulder import parse_prefold_input

dat = parse_prefold_input(open("prefold_input.txt").read())
print("Sequence:", dat["seq"][:40], "...")
print("Temp:", dat["temp"])

API modules

Module	Purpose
primer3plus_core.boulder	Boulder-IO parsing, normalisation, tag injection, primer counting
primer3plus_core.runner	run_primer3(), run_unafold(), run_amplicon3() — subprocess with timeout
primer3plus_core.files	UUID helpers, work-directory creation, path builders
primer3plus_core.settings	Load settings JSON files shipped with the package
primer3plus_core.logging	Run-logging helper (IP/UA passed by caller)
primer3plus_core.models	RunError exception, result dataclasses
primer3plus_core.config	Paths and constants

Development

pip install -e ".[dev]"
python -m pytest tests/ -v

License

GPL-3.0-or-later — same as Primer3Plus.