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primer3-py

Simple oligo analysis and primer design

https://github.com/libnano/primer3-py

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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  • ○
    Scientific vocabulary similarity
    Low similarity (9.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Simple oligo analysis and primer design

Basic Info
Statistics
  • Stars: 180
  • Watchers: 14
  • Forks: 43
  • Open Issues: 2
  • Releases: 32
Created over 12 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License Authors

README.md

primer3-py: simple oligo analysis and primer design

Tests Documentation Release License PyPi

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:

```python

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) ```

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

```python 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

Owner

  • Name: libnano
  • Login: libnano
  • Kind: organization

High performance tooling for nucleic acid design

GitHub Events

Total
  • Create event: 14
  • Release event: 2
  • Issues event: 16
  • Watch event: 14
  • Delete event: 9
  • Issue comment event: 30
  • Push event: 71
  • Pull request review comment event: 18
  • Pull request review event: 27
  • Pull request event: 21
  • Fork event: 1
Last Year
  • Create event: 14
  • Release event: 2
  • Issues event: 16
  • Watch event: 14
  • Delete event: 9
  • Issue comment event: 30
  • Push event: 71
  • Pull request review comment event: 18
  • Pull request review event: 27
  • Pull request event: 21
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 323
  • Total Committers: 4
  • Avg Commits per committer: 80.75
  • Development Distribution Score (DDS): 0.313
Past Year
  • Commits: 40
  • Committers: 2
  • Avg Commits per committer: 20.0
  • Development Distribution Score (DDS): 0.3
Top Committers
Name Email Commits
benpruitt b****t@g****m 222
Nick Conway a****r@g****m 85
Tom Soulanille s****l@p****m 13
Tim D. Smith t****m@b****m 3
Committer Domains (Top 20 + Academic)
borealgenomics.com: 1 prama.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 78
  • Total pull requests: 89
  • Average time to close issues: 6 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 61
  • Total pull request authors: 12
  • Average comments per issue: 2.81
  • Average comments per pull request: 0.61
  • Merged pull requests: 78
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 8
  • Pull requests: 22
  • Average time to close issues: 23 days
  • Average time to close pull requests: 17 days
  • Issue authors: 7
  • Pull request authors: 2
  • Average comments per issue: 1.88
  • Average comments per pull request: 0.59
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • kevin2022lee (4)
  • martinfthomsen (4)
  • peterjc (3)
  • billzt (3)
  • GuoYu-Peng (3)
  • ChrisgKent (2)
  • juechenyang (2)
  • wpwupingwp (2)
  • danxfreeman (1)
  • sanjaynagi (1)
  • yangtcai (1)
  • Lcarey (1)
  • lrm19851015 (1)
  • jonathanronen (1)
  • DNAanalytics (1)
Pull Request Authors
  • grinner (39)
  • benpruitt (38)
  • peterjc (6)
  • liuxiawei (2)
  • dependabot[bot] (2)
  • pramasoul (2)
  • smsaladi (1)
  • tdsmith (1)
  • Permafacture (1)
  • hartzell (1)
  • jsnedeco (1)
  • pessoa-am (1)
Top Labels
Issue Labels
question (1) enhancement (1) wontfix (1) bug (1)
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 25,150 last-month
  • Total docker downloads: 22
  • Total dependent packages: 18
  • Total dependent repositories: 48
  • Total versions: 35
  • Total maintainers: 2
pypi.org: primer3-py

Simple primer design and analysis

  • Versions: 35
  • Dependent Packages: 18
  • Dependent Repositories: 48
  • Downloads: 25,150 Last month
  • Docker Downloads: 22
Rankings
Dependent packages count: 0.8%
Dependent repos count: 2.1%
Downloads: 3.6%
Average: 3.8%
Docker downloads count: 3.8%
Forks count: 6.1%
Stargazers count: 6.1%
Maintainers (2)
grinner benpruitt
Last synced: 11 months ago