Project structure and architecture

Project Structure and architecture

This should be of no concern to the end user but this project is divided into several folders and .py files:

• Images contains images used in this repository
• References contains references folders and related metadata. It also contains the custom_refs folder
  • custom_refs is an empty folder where the user can store their own reference profiles
• tests contains sample files when running run_test
• config
  • MANTIS.cfg config file for Mantis
• mantis contains the all of MANTIS' code
  • cython_src contains the Cython code responsible for compiling the hit extraction algorithm. Cython was used to increase efficiency.
  • __main__.py is the front of the program
  • Assembler.py has all the methods for setting up paths.
  • Consensus.py handles the generation of query sequences consensus. It inherits from UniFunc_wrapper.py. It contains the algorithms for finding the best query hits.
  • Database_generator.py has all the methods for setting up the databases.
  • Exceptions.py contains several custom exceptions
  • Homology_processor.py used for parsing results from HMMER and Diamond
  • MANTIS.py contains main front for launching the annotations, it inherits from all other classes
  • Metadata.py handles the interpretation of the generated annotations. Most references need to be linked to their respective metadata in order to extract usable information.
  • Metadata_SQLITE_Connector.py handles the generation of SQL databases from the metadata.tsv files.
  • Multiprocessing.py contains all the code responsible for multiprocessing
  • Taxonomy_SQLITE_Connector.py handles the SQL databases for the lineage retrieval of NCBI and GTDB taxonomies.
  • UniFunc_wrapper.py wrapper for UniFunc, a text mining tool to measure functional descriptions similarity.
  • utils.py contains small functions that are universal to Mantis