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everest-castaneda / knext

Kyoto Encylopedia of Genes and Genomes (KEGG) NetworkX Topological parser automates downloading, parsing, and converting from a KEGG Markup Language File to a TSV file that is usable in network analyses.
MIT License
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Knext #1

Closed FDUguchunhui closed 6 months ago

FDUguchunhui commented 6 months ago

Refactor code by modularity and encapsulation.

  1. Remove more than 1000 lines of repeated code
  2. Modularize code into functions that are easy to debug and reuse
  3. Create an object to better organize and maintain methods and properties used during parsing KGML (object-oriented Programming)
  4. Replace unnecessary deep nested if-else statements in deciding what code to run with different combinations of options with wrapper function handling options automatically
  5. Unify "genes" and "mixed" functionality under one parser object and keep the original usage by wrapper functions
  6. All functionality should be exactly the same as before, with only the change to using compound KEGG name+entry ID (e.g. cpd:C00022-102) instead of just entry ID (e.g. 102) for better output format.