Using agfusion build command for ensembl >v95?

[min-codes]

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

[murphycj]

Hi Min,

Thanks for using AGFusion.

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

This command was not really meant to be used by users (just me), so I did not add any documentation for it. I'll add some documentation.

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

At the moment, going higher than 95 will cause an error. I'll need to build the databases to go up to 109. I will do this.

[min-codes]

Thank you for your reply - looking forward to the updates 😄

[min-codes]

@murphycj Also - does AGFusion take input from INTEGRATE? There is a 'fusion.bedpe.annot' in the example data directory that looks alot like INTEGRATE output file

[anoronh4]

i am also interested in AGFusion supporting >95. Is there any hope of this update coming soon?

[murphycj]

I added support up to version 111, which is the current max supported by pyensembl. You can try it by updating AGFusion to v1.4.3. Let me know if you have any issues.