https://github.com/Tharos-ux/gfagraphs

Library to parse, edit and handle in memory GFA graphs
https://github.com/Tharos-ux/gfagraphs

pangenome pangenome-graph pangenomics variation-graph variation-graphs

Last synced: 2 months ago
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Library to parse, edit and handle in memory GFA graphs

• Host: GitHub
• URL: https://github.com/Tharos-ux/gfagraphs
• Owner: Tharos-ux
• License: agpl-3.0
• Created: 2023-02-08T10:11:33.000Z (over 1 year ago)
• Default Branch: gfagraphs
• Last Pushed: 2024-07-17T08:49:47.000Z (3 months ago)
• Last Synced: 2024-07-18T09:22:11.466Z (3 months ago)
• Topics: pangenome, pangenome-graph, pangenomics, variation-graph, variation-graphs
• Language: Python
• Homepage: https://tharos-ux.github.io/pangenome-notes/
• Size: 229 KB
• Stars: 2
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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• awesome-pangenomes - gfagraphs

README

        
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[![Documentation Status](https://readthedocs.org/projects/gfagraphs/badge/?version=latest)](https://gfagraphs.readthedocs.io/en/latest/?badge=latest)

# GFAGraphs - A Python GFA library

> [!WARNING]\

> A paper is in preparation about this work. If you consider to use this tool, please contact the author for attribution.

This Python library aims to be an abstraction layer for GFA file format.

> [!WARNING]\

> The old version of `gfagraphs` has been deprecated (since v0.3.0), in favour of `pgGraphs`. Using `gfagraphs` or `pgGraphs` to import resolves now in using the same library. In a near future, `pgGraphs` namespace will be deprecated.

## Package `pgGraphs`/`gfagraphs`

![](https://media.discordapp.net/attachments/874430800802754623/1179353568105467964/library.png)

The package is organized in 4 modules:

+ `gfagraphs.abstractions` contains abstractions over GFA formats

+ `gfagraphs.gfaparser` contains an abstract class for parsing and saving GFA file format

+ `gfagraphs.graph` contains the main `Graph` class that represents a GFA graph in memory, and edit functions

+ `gfagraphs.networkx` conains an abstract class for visualization and modelization of GFA in a NetworkX object

> [!NOTE]\

> Want to contribute? Feel free to open a PR on an issue about a missing, buggy or incomplete feature!