Primer3-py documentation

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 extremely simple:

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

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

In [1]: import primer3

In [2]: %timeit primer3.calcTm('GTAAAACGACGGCCAGT')
100000 loops, best of 3: 4.74 µs per loop

In [3]: %timeit primer3.wrappers.calcTm('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, but you don’t have to deal with messy and slow file IO for your automated workflows.

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: http://primer3.sourceforge.net/.

A copy of the Primer3 2.3.7 design parameters manual can be found at: http://git.io/vnqBx

Indices and tables