Simple interaction to create MSAs with constant depth #1
Description
Dear MSAGPT authors,
It brings me great joy to see research being conducted in creating synthetic MSAs especially with such a nice entry as yours!
I would like to use your MSAGPT as a competitive baseline in a project of mine. For that, I need to generate thousands of MSAs with 128 rows using a single sequence as input for each MSA, which I can do on my own server.
E.g.
bash create_sequence.sh –file_with_query_sequences file.fasta
→ for every sequence in the fasta file a separate MSA file with 128 rows and query on top.
As I can see, there is still some work on the interface going on, which focuses mostly on interactions, but I would like to use a simpler version. Could you create a straight-forward script that would solve my simple interaction? Else, can you point me to some functions in utils/chat.py and parameters like beam size so I could create this script by myself?
Thanks and kind regards,
Jannik
P.S. It would be nice-to-have if I could disable inserts, but there should be something I can do about that in post-processing.