Colab initialization

!pip3 install -U pip > /dev/null
!pip3 install -U "bio-embeddings[all] @ git+https://github.com/sacdallago/bio_embeddings.git" > /dev/null

Embed a sequence passed as a string

import numpy as np
from bio_embeddings.embed import SeqVecEmbedder, ProtTransBertBFDEmbedder

embedders = []
sequence = "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEVVKSGRFVTVQTISGTGALRIGASFLQRFFKFSRDVFLPKPSWGNHTPIFRDAGMQLQSYRYYDPKTCGFDFTGALEDISKIPEQSVLLLHACAHNPTGVDPRPEQWKEIATVVKKRNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSYAKNMGLYGERVGAFTVICKDADEAKRVESQLKILIRPMYSNPPIHGARIASTILTSPDLRKQWLQEVKGMADRIIGMRTQLVSNLKKEGSTHSWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMTKDGRISVAGVTSGNVGYLAHAIHQVTK"

embedders.append(ProtTransBertBFDEmbedder())
embedders.append(SeqVecEmbedder())

embeddings = []
for embedder in embedders:
    embedding = embedder.embed(sequence)
    embeddings.append(embedding)

for embedding in embeddings:
    print(np.array(embedding).shape)