Migrating from v2 to v3
There are major changes from v2 to v3 of MAVIS.
Tab File Headers
Tab file headers no longer start with
#. Any lines starting with a pound will be treated
as comments. This will apply to mavis-style inputs as well as any tab delimited
MAVIS no longer uses command line arguments, config files, and environment variables for configuration. Instead all configurable settings are controlled via a single input JSON config file
MAVIS is now integrated with snakemake instead of handling its own scheduling
Reference Annotation Files
MAVIS no longer supports the previously deprecated tab-delimited format of the annotations file. If you are still using these files in your project we have provided a script to automatically convert them to the newer format in the tools directory.
python src/tools/convert_annotations_format.py \ /path/to/tab/file.tab \ --input_type v2-tab \ /path/to/new/json/file.json
In v3 the JSON files are slightly different to support multiple translations per transcript. You old v3 files can be automatically converted to the new format with the same script
python src/tools/convert_annotations_format.py \ /path/to/json/file.json \ --input_type v2-json \ /path/to/new/json/file.json