AGFusion icon indicating copy to clipboard operation
AGFusion copied to clipboard

Using agfusion build command for ensembl >v95?

Open min-codes opened this issue 1 year ago • 3 comments

Hi Dr. Charles Murphy,

Thank you for developing AGFusion and making it publicly available.

I would like to use agfusion for ensembl >v95, and it seems

1. I will have to build the database myself using agfusion build

usage: agfusion build [-h] -d DIR -s SPECIES -r RELEASE --pfam PFAM [--server SERVER]

May I know if documentation of this command is available? (ie. what sort of file is expected as input for the --pfam option? I looked at http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam35.0/ but unsure which file to use)

2. I will need to manually edit the 'max ensembl version' from 95 to 109 in utils.py

Would this be a correct thing to do - as the current allowed max is v95?

Thank you, Min

min-codes avatar May 24 '23 04:05 min-codes