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 loopPrimer3-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
For documentation of the bindings, see https://libnano.github.io/primer3-py