Package Health Score

50 / 100

security
Security review needed
popularity
Limited
maintenance
Sustainable
community
Limited

Popularity

Limited

GitHub Stars: 48
Forks: 15
Contributors: 4

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package phigaro, we found that it has been starred 48 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Jan 8, 2024
Direct Vulnerabilities: 0
C
0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 0
H
0
M
0
L

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

License

MIT

Security Policy

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Maintenance

Sustainable

Commit Frequency

Open Issues: 3
Open PR: 0
Last Release: 11 months ago
Last Commit: 11 months ago

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

We found that phigaro demonstrates a positive version release cadence with at least one new version released in the past 12 months.

In the past month we didn't find any pull request activity or change in issues status has been detected for the GitHub repository.

Community

Limited

Readme: Yes
Contributing.md: No
Code of Conduct: No
Contributors: 4
Funding: No

This project has seen only 10 or less contributors.

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Package

Python Versions Compatibility: Unspecified

Age: 7 years
Latest Release: 11 months ago
Dependencies: 13 Direct / 18 Total
Versions: 34
Maintainers: 3
Wheels: OS Independent

Readme

Phigaro v2.4.0

Conda installation

Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated “prophage genome maps” and marks possible transposon insertion spots inside prophages. It is applicable for mining prophage regions from large metagenomic datasets.

Updates tracker

You can find the information about updates and releases by link.

Documentation: Installation & Usage

Please, follow the documentation link to find installation and usage information.

Methods overview

Open-reading frames (i.e. proteins) are predicted from the input FASTA file using Prodigal. Phage genes are annotated with prokaryotic viral orthologous groups (pVOGs) profile Hidden Markov Models (HMMs), which can be downloaded stand-alone from http://dmk-brain.ecn.uiowa.edu/pVOGs/. Each contig is represented as a sequence of phage and non-phage genes. A smoothing window algorithm (a triangular window function) determines regions with a high density of phage genes and therefore the prophage regions and boundaries, considering the pVOG annotations and the GC content.

Known issues

Phigaro is tested on Linux systems. For MacOS, you may need to add the following softlink ln -s /usr/libexec/locate.updatedb /usr/local/bin/updated and run brew install wget. If you encounter any issues while running Phigaro on test data, please report them to us at estarikova@rcpcm.org.

Publication

Elizaveta V. Starikova, Polina O. Tikhonova, Nikita A. Prianichnikov, Chris M. Rands, Evgeny M. Zdobnov, Vadim M. Govorun
Phigaro: high throughput prophage sequence annotation

Bioinformatics, 2020; doi: https://doi.org/10.1093/bioinformatics/btaa250
bioRxiv, 2019; doi: https://doi.org/10.1101/598243

phigaro dependencies

argparse beautifulsoup4 biopython bs4 future lxml numpy pandas plotly pyyaml sh singleton six

FAQs

What is phigaro?

Phigaro is a scalable command-line tool for predicting phages and prophages. Visit Snyk Advisor to see a full health score report for phigaro, including popularity, security, maintenance & community analysis.

Is phigaro popular?

The python package phigaro receives a total of 254 weekly downloads. As such, phigaro popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is phigaro well maintained?

We found indications that phigaro maintenance is sustainable demonstrating some project activity. We saw a total of 4 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is phigaro safe to use?

While scanning the latest version of phigaro, 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 25 November-2024, at 20:52 (UTC).

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phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages. 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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Maintenance

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Community

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Package

Readme

Phigaro v2.4.0

Updates tracker

Documentation: Installation & Usage

Methods overview

Known issues

Publication

phigaro dependencies

FAQs

What is phigaro?

Is phigaro popular?

Is phigaro well maintained?

Is phigaro safe to use?

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Package Health Score

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Commit Frequency

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Readme

Phigaro v2.4.0

Updates tracker

Documentation: Installation & Usage

Methods overview

Known issues

Publication

phigaro dependencies

FAQs

What is phigaro?

Is phigaro popular?

Is phigaro well maintained?

Is phigaro safe to use?

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Source Code

Open Source

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Config

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