geneformer/__init__.py

# ruff: noqa: F401
import warnings
from pathlib import Path

warnings.filterwarnings("ignore", message=".*The 'nopython' keyword.*")  # noqa # isort:skip

GENE_MEDIAN_FILE = Path(__file__).parent / "gene_median_dictionary_gc104M.pkl"
TOKEN_DICTIONARY_FILE = Path(__file__).parent / "token_dictionary_gc104M.pkl"
ENSEMBL_DICTIONARY_FILE = Path(__file__).parent / "gene_name_id_dict_gc104M.pkl"
ENSEMBL_MAPPING_FILE = Path(__file__).parent / "ensembl_mapping_dict_gc104M.pkl"

GENE_MEDIAN_FILE_30M = Path(__file__).parent / "gene_dictionaries_30m/gene_median_dictionary_gc30M.pkl"
TOKEN_DICTIONARY_FILE_30M = Path(__file__).parent / "gene_dictionaries_30m/token_dictionary_gc30M.pkl"
ENSEMBL_DICTIONARY_FILE_30M = Path(__file__).parent / "gene_dictionaries_30m/gene_name_id_dict_gc30M.pkl"
ENSEMBL_MAPPING_FILE_30M = Path(__file__).parent / "gene_dictionaries_30m/ensembl_mapping_dict_gc30M.pkl"

from . import (
    collator_for_classification,
    emb_extractor,
    in_silico_perturber,
    in_silico_perturber_stats,
    pretrainer,
    tokenizer,
)
from .collator_for_classification import (
    DataCollatorForCellClassification,
    DataCollatorForGeneClassification,
)
from .emb_extractor import EmbExtractor, get_embs
from .in_silico_perturber import InSilicoPerturber
from .in_silico_perturber_stats import InSilicoPerturberStats
from .pretrainer import GeneformerPretrainer
from .tokenizer import TranscriptomeTokenizer

from . import classifier  # noqa # isort:skip
from .classifier import Classifier  # noqa # isort:skip

from . import mtl_classifier  # noqa # isort:skip
from .mtl_classifier import MTLClassifier  # noqa # isort:skip