dudes revision

[pirovc]

Due to the recent update to v0.10.0, promising results with metaproteomics data (thanks to @rababerladuseladim) and the potential to use of the core methodology from DUDes in different applications, I suggest a couple of changes and features for this repository:

• code refactoring
  • simplification in many areas, removal of unnecessary classes and better structure
  • use of multitax to handle taxonomy. This will simplify a good part of the code and allow usage of the method with many other existing and custom taxonomies (e.g. GTDB)
  • removal of GI support for genomic data, since it is long outdated
  • properly parse acc2txid files similar to this.
  • re-evaluate the role and necessity of having a dudesdb
• generalization of the deepest uncommon descendant (DUD) method
  • independence of input data type
  • standardize the inputs and outputs for the core method
  • create standard modules for specific data types, for example the parse_sam.py for metagenomics and parse_diamond_blast.py for metaproteomics, which could be easily extended to other types
  • possibility to input raw text data
• infrastructure
  • increase and improve testing and CI
  • documentation