Index

A

Alignment (class in plast.alignment)

assign_eggnog_annot() (plast.plast.PLAST method) assign_mmseqs_clusters() (plast.plast.PLAST method)

B

BadToken

best_layout_min_crossings() (in module plast.alignment)

C

copy() (plast.plast.PLAST method)

cosine_similarity_numba() (in module plast.utils) count_inversions() (in module plast.alignment)

D

DataLoadingError

debug() (plast.plast.PLAST method) draw_network() (plast.plast.PLAST method)

E

embeddings (plast.model.PLASTModel property) encode() (plast.plast.PLAST method)

error() (plast.plast.PLAST method) euclidean() (in module plast.utils) extract_module_pairs() (in module plast.alignment)

F

from_dict() (plast.plast.PLAST static method)

from_json() (plast.plast.PLAST static method)

G

get_by_accession() (plast.plast.PLAST static method)

get_model() (plast.data.PLASTData method) get_most_similar() (plast.plast.PLAST method)

I

idf (plast.model.PLASTModel property)

is_gpu_available() (in module plast.utils) is_unknown() (in module plast.alignment)

L

load_gbff() (plast.plast.PLAST method)

load_nt_fasta() (plast.plast.PLAST method) log() (plast.plast.PLAST method)

M

mapping_and_crossings() (in module plast.alignment) mean_embedding (plast.model.PLASTModel property) model (plast.model.PLASTModel property) module plast.alignment plast.data plast.exceptions plast.model plast.parsers plast.plast plast.utils

N

NotFoundError

P

PLAST (class in plast.plast) plast.alignment module plast.data module plast.exceptions module plast.model module

plast.parsers module plast.plast module plast.utils module PLASTData (class in plast.data) PLASTModel (class in plast.model)

R

read_emapper_hits() (in module plast.parsers) read_fasta() (in module plast.parsers) read_gbff() (in module plast.parsers) read_hmmscan_output() (in module plast.parsers)

read_m8() (in module plast.parsers) rotate() (in module plast.alignment) rotate_parsed() (in module plast.alignment) rotate_plasmid() (in module plast.alignment)

T

tmp_dir() (plast.plast.PLAST method)

to_dict() (plast.plast.PLAST method) to_json() (plast.plast.PLAST method)

U

umap_mapper (plast.model.PLASTModel property)

W

warm_page_cache() (in module plast.utils)