Database for MMseqs2 searchh

[d-courtine]

State of the art

For the moment, a user can pass 3 different values to --mmseqs-search-db for the reference database:

1. A path to a valid MMseq database, present somewhere in the system
2. A FastA/Q[.gz] file, KRYPTON setup the database from this file. The database is stored in the current project, provided by --out
3. The name of a database that can be downloaded with mmseqs database. The database is stored in the current project too.

Problematic

If the user provides option 2. or 3., and this for X samples, this means that KRYPTON will run X times the steps for the database setup and download. This can be a bottleneck and I do not want this to happen.

Solution

• Add another parameter, eg --user-db-path, which accepts a path on the system where the user wants to store and save a given database.

It will work as:

• A valid database is passed to --mmseqs-search-db -> ignore --user-db-path
• A FastA/Q file is passed to --mmseqs-search-db -> do --user-db-path contains a valid path?
  • No: setup the database within the project (--out)
  • Yes: Do a database with this name already exists in the directory --user-db-path ?
    • No: setup the database here
    • Yes: Perfect, use this path for the reference database
• A valid name for the downloadable by MMseqs2 is passed to --mmseqs-search-db -> Same as for FastA file