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gfagraphs's Introduction

Documentation Status

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!

gfagraphs's People

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gfagraphs's Issues

Improving graph structure

It has been asked to add method for starting and ending nodes search, as well as a graph initialisation method of the NetworkX structure without edge duplicates to help with usage of the lib.

Pre 3.10 compatible?

Hi,

I am interested in trying out your tool. I wonder if there is anything in the code that is not compatible with earlier python versions than 3.10, and if not, whether you could update the package in the index. I could get my hands dirty and just use/adapt the sources, but I'd like to just install a compatible version from pypi.

thanks

Handling nodes of pangraph

Pangraph appears to be using chars as node identifiers. As of now, the tool strips characters to keep digits, and use integers to walk through the graph.

Potential fix : use int <-> node name mapping in such cases

Clear separation between parsing and visualisation

As pinpointed in #1, it happens that those two concepts aren't connected thus they are in the code. This issue needs to address this.

TODO

  • NetworkX representation should be disconnected to visualization, but still be its backbone
  • A more clear documentation on how to use those functions should be made

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