Skip to main content

Python bindings for Primer3

Project description

https://secure.travis-ci.org/libnano/primer3-py.png https://img.shields.io/pypi/l/primer3-py.png https://img.shields.io/pypi/v/primer3-py.png

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.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 us 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.

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: https://git.io/v9xrc

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

Project details


Release history Release notifications

This version
History Node

0.5.5

History Node

0.5.4

History Node

0.5.3

History Node

0.5.2

History Node

0.5.1

History Node

0.5.0

History Node

0.4.3

History Node

0.4.2

History Node

0.4.1

History Node

0.4.0

History Node

0.3.1

History Node

0.3.0

History Node

0.2.5

History Node

0.2.4

History Node

0.2.3

History Node

0.2.2

History Node

0.2.1

History Node

0.2

History Node

0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
primer3_py-0.5.5-cp27-cp27m-macosx_10_7_x86_64.whl (513.6 kB) Copy SHA256 hash SHA256 Wheel cp27 Oct 30, 2017
primer3_py-0.5.5-cp35-cp35m-macosx_10_6_x86_64.whl (511.6 kB) Copy SHA256 hash SHA256 Wheel cp35 Oct 30, 2017
primer3_py-0.5.5-cp36-cp36m-macosx_10_7_x86_64.whl (511.6 kB) Copy SHA256 hash SHA256 Wheel cp36 Oct 30, 2017
primer3-py-0.5.5.tar.gz (390.3 kB) Copy SHA256 hash SHA256 Source None Oct 30, 2017

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page