Revamping the module for filling gaps

[GwennyGit]

For the following reasons the module for gap-filling needs to be revamped:

• SPECIMEN's extension module and the module for gap filling within refineGEMs have some similarities/overlaps ($\rightarrow$ see Analysis of module extension SPECIMEN#9) and could, thus, be combined.
• The gap-filling module within refineGEMs needs an overhaul with respect to some of its functionalities, as well as the overall set-ups ($\rightarrow$ see Improvement of gap-filling in refineGEMs #52), and the same is true for the extension module in SPECIMEN ($\rightarrow$ see Improvement of the extension module SPECIMEN#3).

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Todo:

• 🗄️ Reorganise gap filling as class set-up
  • Implement an abstract core class for gap analysis (GapFiller)
    • Determine which methods should be abstract & which should be already fully implemented $\rightarrow$ Fill classes with information from the OG modules
    • 📂 Output for gap analysis: Folder with several TSV/CSV files
  • Implement one class per analysis set-up: KEGGapFiller, BioCycGapFiller, GeneGapFiller
    • Fill classes with functionalities from the OG modules
  • 💡 Separate class for gap filling instead of function gapfill_model
    • 💡 Option to add either all new content from gap analysis to the model or restricted by namespace
    • ✍🏻 Report with statistics (+ some analyses?)
• ❗Realise improvements during revamping