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🔖 Old lib deprecation
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dubssieg committed Apr 19, 2024
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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.
Two implementations are proposed:
+ a legacy one, which will remain until deprecated, in `gfagraphs/`
+ a new, cleaner and faster implementation, in `pgGraphs/`

> [!WARNING]\
> Moving forward, features will only be added to `pgGraphs`, while `gfagraphs` will remain as it, until full migration is done in [pancat](https://github.com/Tharos-ux/pancat) tool.
> 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
## Package `pgGraphs`/`gfagraphs`

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

The package is organized in 4 modules:
+ `pgGraphs.abstractions` contains abstractions over GFA formats
+ `pgGraphs.gfaparser` contains an abstract class for parsing and saving GFA file format
+ `pgGraphs.graph` contains the main `Graph` class that represents a GFA graph in memory, and edit functions
+ `pgGraphs.networkx` conains an abstract class for visualization and modelization of GFA in a NetworkX object
+ `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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