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marschall-lab / gaftools

General purpose utility related to GAF files
https://gaftools.readthedocs.io/
MIT License
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Gfa class #9

Closed fawaz-dabbaghieh closed 1 year ago

fawaz-dabbaghieh commented 1 year ago

I have implemented a GFA class in the GFA.py file, I added it to realign, exactly in the realign_gaf replaced line nodes = gaftools.gaf.parse_gfa(graph, with_sequence=True) with graph_obj = GFA(graph) and replaced path_sequence = gaftools.gaf.get_path(nodes, line.path) with path_sequence = graph_obj.extract_path(line.path)