primer3-py

Name	primer3-py JSON
Version	2.0.3 JSON
	download
home_page	https://github.com/libnano/primer3-py
Summary	Python bindings for Primer3
upload_time	2024-02-16 03:01:12
maintainer
docs_url	None
author	Ben Pruitt, Nick Conway
requires_python
license	GPLv2
keywords
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            ## primer3-py: simple oligo analysis and primer design

<a href="https://github.com/libnano/primer3-py/actions/" rel="actions">![Actions](https://github.com/libnano/primer3-py/actions/workflows/primer3-py-ci-github-action.yml/badge.svg)</a>
<a href="http://www.gnu.org/licenses/gpl-2.0.html" rel="license">![License](https://img.shields.io/pypi/l/primer3-py.png)</a>
<a href="https://pypi.python.org/pypi/primer3-py" rel="pypi">![PyPi](https://img.shields.io/pypi/v/primer3-py.png)</a>


**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)::

```bash
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](https://htmlpreview.github.io/?https://github.com/primer3-org/primer3/blob/v2.6.1/src/primer3_manual.htm)

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

            

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    "description": "## primer3-py: simple oligo analysis and primer design\n\n<a href=\"https://github.com/libnano/primer3-py/actions/\" rel=\"actions\">![Actions](https://github.com/libnano/primer3-py/actions/workflows/primer3-py-ci-github-action.yml/badge.svg)</a>\n<a href=\"http://www.gnu.org/licenses/gpl-2.0.html\" rel=\"license\">![License](https://img.shields.io/pypi/l/primer3-py.png)</a>\n<a href=\"https://pypi.python.org/pypi/primer3-py\" rel=\"pypi\">![PyPi](https://img.shields.io/pypi/v/primer3-py.png)</a>\n\n\n**Primer3-py** is a Python-abstracted API for the popular Primer3 library. The\nintention is to provide a simple and reliable interface for automated oligo\nanalysis and design.\n\nRoutine oligo analysis is simple::\n\n    >>> import primer3\n    >>> primer3.calc_tm('GTAAAACGACGGCCAGT')\n    49.16808228911765\n    >>> primer3.calc_hairpin('CCCCCATCCGATCAGGGGG')\n    ThermoResult(structure_found=True, tm=34.15, dg=337.09, dh=-36300.00, ds=-118.13)\n\n... and `fast` (**~1000X** faster than traditional subprocess wrappers)::\n\n```bash\nIn [1]: import primer3\n\nIn [2]: import tests.wrapper\n\nIn [3]: %timeit primer3.calc_tm('GTAAAACGACGGCCAGT')\n100000 loops, best of 3: 4.74 us per loop\n\nIn [4]: %timeit test.wrappers.calc_tm('GTAAAACGACGGCCAGT')\n100000 loops, best of 3: 5.78 ms per loop\n```\n\n**Primer3-py** also includes bindings for the Primer3 `primer design engine`\nif you'd prefer to use an established pipeline. The IO parameters mirror those\nof the original Primer3.\n\n**Please note that while we provide bindings, we do not provide support for\nthe Primer3 design engine. Please contact the Primer3 dev team with your\nquestions: https://github.com/primer3-org/primer3 **\n\nA copy of the Primer3 2.6.1 design parameters manual can be found at:\n[primer3 v2.6.1 manual](https://htmlpreview.github.io/?https://github.com/primer3-org/primer3/blob/v2.6.1/src/primer3_manual.htm)\n\nFor documentation of the bindings, see https://libnano.github.io/primer3-py\n",
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