BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.
It's a minor thing, but it gave me a headache for a little while and I needed to dig through the code to see how the path specified via --oasis-db is passed to SQLite.
The CLI --help page suggests to pass paths as sqlite:////Absolute/path/to/oas_human_subject_9mers_2019_11.db, but as can be seen below, the sqlite:/// is already prepended. This results in Error: .. The OASis DB path does not exist ....
It's a minor thing, but it gave me a headache for a little while and I needed to dig through the code to see how the path specified via
--oasis-dbis passed to SQLite.The CLI
--helppage suggests to pass paths assqlite:////Absolute/path/to/oas_human_subject_9mers_2019_11.db, but as can be seen below, thesqlite:///is already prepended. This results inError: .. The OASis DB path does not exist ....https://github.com/Merck/BioPhi/blob/55440a0b6d561375f26d283c7425042ccd084288/biophi/humanization/methods/humanness.py#L297