Scripts folder

genelist_to_panel.py

Used to print to terminal a gene panel based on a gene list.

transfer-archive.py

Used to migrate case info from an old archive to a newer one.

update_files_path.py

Used to change all paths in the database when moving cases's file from one server to another. The scripts checks if cases contain file paths pointing to location in the old server (--test option) and updates these paths to new paths on the new machine.

Usage: bash python --db_uri mongodb_connection_uri -o /old/path/to/files -n /new/path/to/files

options:
--test : Use this flag to test the function
-d: Use this flag to create a list of keys where old path is found

update_variant_panels.py

Update variant panels.