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pygmes

A python wrapper for GeneMark-ES

https://github.com/openpaul/pygmes

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 (3.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A python wrapper for GeneMark-ES

Basic Info
  • Host: GitHub
  • Owner: openpaul
  • License: gpl-3.0
  • Language: AMPL
  • Default Branch: master
  • Size: 1.4 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Archived
Created about 6 years ago · Last pushed over 5 years ago
Metadata Files
Readme License

README.md

pygmes is a wraper for GeneMark-ES

This project aims at making GeneMark-ES more usable. By default GeneMark-ES has some problems with fragmented and incomplete genomes.

For metagenomic analysis this is an issue, thus I developed pygmes.

Status

Currently this project is very much WIP, so do expect problems and incomplete documentation.

It is just on pip already as it is a suggested package for EukCC (https://github.com/Finn-Lab/EukCC/)

Owner

  • Name: Paul
  • Login: openpaul
  • Kind: user
  • Location: Netherlands

Bioinformatician from Germany, now in the Netherlands

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 65
  • Total Committers: 2
  • Avg Commits per committer: 32.5
  • Development Distribution Score (DDS): 0.015
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Paul Saary s****y@e****k 64
Dan Fornika d****a@g****m 1
Committer Domains (Top 20 + Academic)
ebi.ac.uk: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 14 hours
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
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
  • dfornika (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 26 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 9
  • Total maintainers: 3
pypi.org: pygmes

Run GeneMark-ES using pretrained models

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 26 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Forks count: 22.6%
Average: 24.9%
Downloads: 31.4%
Stargazers count: 38.8%
Maintainers (3)
saary kates_ebi Vkale1
Last synced: 10 months ago

Dependencies

setup.py pypi
  • ete3 *