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primer3plus

A easy-to-use Python API for Primer3 primer design.

https://github.com/jvrana/primer3-py-plus

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.2%) to scientific vocabulary

Keywords

biocad biodesign dna molecular-biology
Last synced: 9 months ago · JSON representation

Repository

A easy-to-use Python API for Primer3 primer design.

Basic Info
Statistics
  • Stars: 16
  • Watchers: 1
  • Forks: 6
  • Open Issues: 5
  • Releases: 0
Topics
biocad biodesign dna molecular-biology
Created over 7 years ago · Last pushed over 3 years ago
Metadata Files
Readme

README.md

Primer3Plus

PyPI version Build package Code style: black pre-commit codecov Language grade: Python Total alerts

Primer3Plus is a Python DNA primer design tool based off of Primer3 and the Python primer3 wrapper (https://pypi.org/project/primer3-py/).

```python import json

design = Design() template = """ TCATGTAATTAGTTATGTCACGCTTACATTCACGCCCTCCCCCCAC ATCCGCTCTAACCGAAAAGGAAGGAGTTAGACAACCTGAAGTCTAG GTCCCTATTTATTTTTTTATAGTTATGTTAGTATTAAGAACGTTAT TTATATTTCAAATTTTTCTTTTTTTTCTGTACAGACGCGTGTACGC ATGTAACATTATACTGAAAACCTTGCTTGAGAAGGTTTTGGGACGC TCGAAGGCTTTAATTTGC """ template = template.replace('\n', '').replace(' ', '') design.settings.template(template) design.settings.ascloningtask() design.settings.primernumreturn(1) results, explain = design.run()

print(json.dumps(results, indent=1)) print(json.dumps(explain, indent=1)) ```

json { "0": { "PAIR": { "PENALTY": 11.204301707622733, "COMPL_ANY_TH": 0.0, "COMPL_END_TH": 0.0, "PRODUCT_SIZE": 248 }, "LEFT": { "PENALTY": 9.027129166714644, "SEQUENCE": "TCATGTAATTAGTTATGTCACGCTTAC", "location": [ 0, 27 ], "TM": 57.972870833285356, "GC_PERCENT": 33.333333333333336, "SELF_ANY_TH": 0.0, "SELF_END_TH": 0.0, "HAIRPIN_TH": 0.0, "END_STABILITY": 2.34 }, "RIGHT": { "PENALTY": 2.1771725409080886, "SEQUENCE": "GCAAATTAAAGCCTTCGAGCG", "location": [ 247, 21 ], "TM": 58.82282745909191, "GC_PERCENT": 47.61904761904762, "SELF_ANY_TH": 0.0, "SELF_END_TH": 0.0, "HAIRPIN_TH": 38.006257959698985, "END_STABILITY": 5.03 } } } { "PRIMER_LEFT_EXPLAIN": "considered 10, low tm 9, ok 1", "PRIMER_RIGHT_EXPLAIN": "considered 10, low tm 3, high tm 4, ok 3", "PRIMER_PAIR_EXPLAIN": "considered 1, ok 1", "PRIMER_LEFT_NUM_RETURNED": 1, "PRIMER_RIGHT_NUM_RETURNED": 1, "PRIMER_INTERNAL_NUM_RETURNED": 0, "PRIMER_PAIR_NUM_RETURNED": 1 }

Installation

pip install primer3plus -U

Requirements

python >= 3.5

Owner

  • Name: Justin Vrana
  • Login: jvrana
  • Kind: user
  • Location: Seattle, WA
  • Company: @justevotec

Software Engineer | Just-Evotec Biotherapeutics | PhD @klavinslab

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 110
  • Total Committers: 2
  • Avg Commits per committer: 55.0
  • Development Distribution Score (DDS): 0.009
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Justin Vrana j****a@g****m 109
Justin Vrana j****a@u****u 1
Committer Domains (Top 20 + Academic)
uw.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • jvrana (3)
  • dependabot[bot] (2)
  • lgtm-com[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 115 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 12
  • Total maintainers: 1
pypi.org: primer3plus

An easy-to-use Python API for Primer3 primer design.

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 115 Last month
Rankings
Dependent repos count: 9.0%
Dependent packages count: 10.0%
Forks count: 13.3%
Average: 15.0%
Stargazers count: 16.5%
Downloads: 26.1%
Maintainers (1)
jvrana
Last synced: 10 months ago