Generating fixed-length embeddings from fastafile

[Aurelien-Pelissier]

Hi, I generated some embeddings with the function

abmap.augment_from_fasta (fastaPath = fasta_file...)

The embeddings that I obtained are residue-level embeddings, what arguments should I pass to obtain fixed-length embeddings ?

Thanks you

[lordim]

Hello, so augmentation is part of the process for generating AbMAP embeddings. After you augment a sequence using augment_from_fasta, you need to take that embedding as input to the pre-trained AbMAP models in order to generate either fixed-length or residue-length embeddings. If you would like to do the entire process at once, you can check out the abmap.abmap_embed function.