diff --git a/biomni/tool/genomics.py b/biomni/tool/genomics.py index d84d26bc..60203c43 100644 --- a/biomni/tool/genomics.py +++ b/biomni/tool/genomics.py @@ -1,16 +1,12 @@ import os from pathlib import Path -import esm import gget -import gseapy import numpy as np import pandas as pd import requests import scanpy as sc import torch -from pybiomart import Dataset -from tqdm import tqdm from biomni.llm import get_llm @@ -152,6 +148,7 @@ def interspecies_gene_conversion( >>> print(result) Gene conversion results saved to: human_to_mouse_gene_conversion.csv """ + from pybiomart import Dataset steps = [] @@ -336,6 +333,9 @@ def generate_gene_embeddings_with_ESM_models( Returns: String containing the steps performed during the embedding generation process """ + import esm + from tqdm import tqdm + steps = [] steps.append(f"Loading ESM model: {model_name}") # model loading take a while, once loaded for smaller models generation is relatively fast @@ -1015,6 +1015,8 @@ def get_rna_seq_archs4(gene_name: str, K: int = 10) -> str: def get_gene_set_enrichment_analysis_supported_database_list() -> list: + import gseapy + return gseapy.get_library_name()