Package Health Score

66 / 100

security
Security review needed
popularity
Limited
maintenance
Healthy
community
Sustainable

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Popularity

Limited

GitHub Stars: 132
Forks: 13
Contributors: 7

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package Pharokka, we found that it has been starred 132 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Mar 13, 2024
Direct Vulnerabilities: 0
C
0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 3
H
2
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

MIT

Security Policy

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Maintenance

Healthy

Commit Frequency

Open Issues: 12
Open PR: 0
Last Release: 2 months ago
Last Commit: 14 days ago

Further analysis of the maintenance status of Pharokka based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that Pharokka demonstrates a positive version release cadence with at least one new version released in the past 3 months.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Sustainable

Readme: Yes
Contributing.md: Yes
Code of Conduct: No
Contributors: 7
Funding: No

This project has seen only 10 or less contributors.

We found a way for you to contribute to the project! Looks like Pharokka is missing a Code of Conduct.

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Package

Python Versions Compatibility: >=3.5

Age: 8 months
Latest Release: 2 months ago
Dependencies: 15 Direct / 40 Total
Versions: 8
Maintainers: 1
Wheels: OS Independent

Readme

pharokka

pharokka Logo

Extra special thanks to Ghais Houtak for making Pharokka's logo.

Fast Phage Annotation Tool

pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.

If you are looking for rapid standardised annotation of bacterial genomes, please use Bakta. Prokka, which inspired the creation and naming of pharokka, is another good option, but Bakta is Prokka's worthy successor.

phold

If you like pharokka, you will probably love phold. phold uses structural homology to improve phage annotation. Benchmarking is ongoing but phold strongly outperforms pharokka in terms of annotation, particularly for less characterised phages such as those from metagenomic datasets.

pharokka still has features phold lacks for now (identifying tRNA, tmRNA, CRISPR repeats, and INPHARED taxonomy search), so it it recommended to run phold after running pharokka.

phold takes the Genbank output of Pharokka as input. Therefore, if you have already annotated your phage(s) with Pharokka, you can easily update the annotation with more functional predictions with phold.

Google Colab Notebooks

If you don't want to install pharokka or phold locally, you can run pharokka and phold, or only pharokka, without any code using the Google Colab notebook https://colab.research.google.com/github/gbouras13/pharokka/blob/master/run_pharokka_and_phold.ipynb

Quick Start

The easiest way to install pharokka is via conda:

conda install -c bioconda pharokka

Followed by database download and installation:

`install_databases.py -o

Pharokka dependencies

alive-progress bcbio-gff biopython black isort loguru pandas pyhmmer pyrodigal pyrodigal-gv pytest pytest-cov pyyaml requests setuptools

FAQs

What is Pharokka?

Fast phage annotation tool. Visit Snyk Advisor to see a full health score report for Pharokka, including popularity, security, maintenance & community analysis.

Is Pharokka popular?

The python package Pharokka receives a total of 453 weekly downloads. As such, Pharokka popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is Pharokka well maintained?

We found that Pharokka demonstrated a healthy version release cadence and project activity. It has a community of 7 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is Pharokka safe to use?

While scanning the latest version of Pharokka, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 4 May-2024, at 03:07 (UTC).

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Pharokka

Fast phage annotation tool For more information about how to use this package see README

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Package Health Score

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Security

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Community

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Package

Readme

pharokka

Fast Phage Annotation Tool

phold

Google Colab Notebooks

Table of Contents

Quick Start

Pharokka dependencies

FAQs

What is Pharokka?

Is Pharokka popular?

Is Pharokka well maintained?

Is Pharokka safe to use?

Build a secure application checklist

Select a recommended open source package

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Fix identified vulnerabilities

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Package Health Score

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Direct Usage Popularity

Security and license risk for latest version

Commit Frequency

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Readme

pharokka

Fast Phage Annotation Tool

phold

Google Colab Notebooks

Table of Contents

Quick Start

Pharokka dependencies

FAQs

What is Pharokka?

Is Pharokka popular?

Is Pharokka well maintained?

Is Pharokka safe to use?

Build a secure application checklist

Select a recommended open source package

Scan your app for vulnerabilities

Source Code

Open Source

Container

Config

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