primer3-py

primer3-py: simple oligo analysis and primer design

Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

Routine oligo analysis is simple:

>>> import primer3
>>> primer3.calc_tm('GTAAAACGACGGCCAGT')
49.16808228911765
>>> primer3.calc_hairpin('CCCCCATCCGATCAGGGGG')
ThermoResult(structure_found=True, tm=34.15, dg=337.09, dh=-36300.00, ds=-118.13)

... and fast (~1000X faster than traditional subprocess wrappers):

In [1]: import primer3

In [2]: import tests.wrapper

In [3]: %timeit primer3.calc_tm('GTAAAACGACGGCCAGT')
100000 loops, best of 3: 4.74 us per loop

In [4]: %timeit test.wrappers.calc_tm('GTAAAACGACGGCCAGT')
100000 loops, best of 3: 5.78 ms per loop

Primer3-py also includes bindings for the Primer3 primer design engine if you'd prefer to use an established pipeline. The IO parameters mirror those of the original Primer3.

Please note that while we provide bindings, we do not provide support for the Primer3 design engine. Please contact the Primer3 dev team with your questions: https://github.com/primer3-org/primer3

A copy of the Primer3 2.6.1 design parameters manual can be found at: primer3 v2.6.1 manual

Documentation

• API Documentation
• Quick Start Guide
• Development Guide
• Release Process