primer3-py

library2.3.0pypypi✓ verified 87d ago

Python bindings for the Primer3 primer design and analysis library. Current version 2.3.0 supports Python 3.8–3.14. Actively maintained, with occasional releases.

ai-ml data serialization

pip install primer3-py

github ↗package ↗docs ↗

INSTALL

IMPORT

SIG · PRIMER3-PY

primer3-py

ai-mlpythonv2.3.0

Install

1.7s avg

Import

40ms

Disk

28MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v2.3.0 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 1.7s · import 0.040s · 30MB

28MB installed

● package 28MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

bindings

✓ import primer3

✗ from primer3 import *

Wildcard imports discouraged; use explicit import.

Calculate Tm of a DNA sequence.

import primer3 seq = 'AGCAGCGCGTATACGCGTATATACGCGATATCGCGTAGCT' result = primer3.calc_tm(seq) print(result)

Debug

Known issues

breakingIn v2.0.0, the output dictionary keys changed: list versions of PRIMER_PAIR, PRIMER_LEFT, PRIMER_RIGHT, PRIMER_INTERNAL were added. Code relying on old key shapes may break if not adapted.

fix

Use both old and new keys or update code to use list versions.

affects: >=2.0.0

breakingIn v1.0.0, setGlobals was removed; use primer3.set_global_flags or direct parameter passing instead.

fix

Replace primer3.setGlobals(...) with primer3.set_global_flags(...) or pass parameters as dict.

affects: >=1.0.0

gotchacalc_tm accepts sequences with ambiguous bases (e.g., 'N') but may raise exceptions for invalid characters. Ensure input is valid DNA.

fix

Validate or sanitize sequences before passing to calc_tm.

affects: all

Errors

Common errors & fixes

AttributeError: module 'primer3' has no attribute 'setGlobals'

setGlobals was removed in v1.0.0.

fix

Use primer3.set_global_flags(parameters) instead.

TypeError: calc_tm() got an unexpected keyword argument 'mv_conc'

calc_tm uses keyword arguments for salt and divalent concentrations; incorrect param name.

fix

Use valid keyword arguments: mv_conc, dv_conc, dntp_conc, dna_conc.

ValueError: Sequence 'XYZ' contains invalid characters

Sequence contains non-DNA letters or whitespace.

fix

Clean sequence with primer3.clean_sequence(seq) or validate manually.

Upgrade

Version history

2.3.0latest on PyPI · released Jan 6, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

2 hits · last 30 days

node

Resources

githubhttps://github.com/libnano/primer3-py ↗

packagehttps://pypi.org/project/primer3-py/ ↗

docshttp://libnano.github.io/primer3-py ↗