evolocity.pp.featurize_fasta¶
-
evolocity.pp.
featurize_fasta
(fname, model_name='esm1b', mkey='model', embed_batch_size=3000, fasta_metadata_record=False, use_cache=True, cache_namespace=None)¶ Embeds a FASTA file.
Takes a FASTA file containing sequences and returns an
Anndata
object with sequence embeddings in the adata.X matrix.An optional argument (fasta_metadata_record) allows for loading metadata directly from the FASTA file.
- Parameters
- fname : str
Path to FASTA file.
- model_name : str (default: ‘esm1b’)
Language model used to compute likelihoods.
- mkey : str (default: ‘model’)
Name at which language model is stored.
- embed_batch_size : int (default: 3000)
Batch size to embed sequences. Lower to fit into GPU memory.
- fasta_metadata_record : bool (default: False)
If True, assumes metadata is storred in FASTA record as key=value pairs that are separated by vertical bar “|” characters. Otherwise, does not attempt to load metadata from the FASTA.
- use_cache : bool (default: False)
Cache embeddings to disk for faster future loading.
- cache_namespace : str (default: ‘protein’)
Namespace at which to store cache.
- Returns
Returns an
Anndata
object with the attributes.X – Matrix where rows correspond to sequences and columns are language model embedding dimensions
seq (.obs) – Sequences corresponding to rows in adata.X
model (.uns) – language model