https://github.com/dubssieg/gfagraphs

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

pangenome pangenome-graph pangenomics variation-graph variation-graphs

Last synced: about 1 year ago
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Library to parse, edit and handle in memory GFA graphs

• Host: GitHub
• URL: https://github.com/dubssieg/gfagraphs
• Owner: dubssieg
• License: agpl-3.0
• Created: 2023-02-08T10:11:33.000Z (over 3 years ago)
• Default Branch: gfagraphs
• Last Pushed: 2024-08-31T08:28:30.000Z (almost 2 years ago)
• Last Synced: 2024-09-21T01:57:54.857Z (over 1 year ago)
• Topics: pangenome, pangenome-graph, pangenomics, variation-graph, variation-graphs
• Language: Python
• Homepage: https://tharos-ux.github.io/pangenome-notes/
• Size: 251 KB
• Stars: 2
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# GFAGraphs - A Python GFA library

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

> [!WARNING]\

> `gfagraphs` is not actively maintained as I moved to Rust for my main research work. However, as the library is used in some projects, the library remains available as is.

## Package `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!