Library to parse, edit and handle in memory GFA graphs

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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

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!

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