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Dependency on dustdas #400

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anthony-aylward opened this issue Jul 30, 2024 · 0 comments
Open

Dependency on dustdas #400

anthony-aylward opened this issue Jul 30, 2024 · 0 comments

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@anthony-aylward
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anthony-aylward commented Jul 30, 2024 •
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GeenuFF's dependency on dustdas seems like more of a liability than a benefit. It could be refactored with relatively minor changes to remove this dependency. FASTA and GFF parsing can be accomplished by biopython and pandas, while GFF entries can be represented by a named tuple instead of dustdas's GFFObject. See my pull request for such a refactoring that remains correct / passes all unit tests.

Does GeenuFF's functionality depend on dustdas in any more ways that I missed?
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