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Refactor genomics.py: lazy-load optional dependencies #276

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Refactor genomics.py: lazy-load optional dependencies #276

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10 changes: 6 additions & 4 deletions biomni/tool/genomics.py
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Original file line number Diff line number Diff line change
@@ -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

Expand Down Expand Up @@ -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 = []

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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()


Expand Down