File size: 2,702 Bytes
53e66de | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 | #!/usr/bin/env bash
set -euo pipefail
# Batch deterministic inference from a CSV file.
# Run this inside an allocated/interactive GPU session. No SLURM resources are requested here.
PROJECT_DIR="${PROJECT_DIR:-/public/home/scnb9biwet/jiangqq/CodonTransformer-main}"
HF_HOME="${HF_HOME:-/public/home/scnb9biwet/.cache/huggingface}"
CONDA_ENV="${CONDA_ENV:-struct-evo}"
INPUT_CSV="${INPUT_CSV:-${PROJECT_DIR}/scripts/demo/sample_dataset.csv}"
OUTPUT_CSV="${OUTPUT_CSV:-${PROJECT_DIR}/outputs/sample_predictions.csv}"
OFFLINE="${OFFLINE:-1}"
cd "${PROJECT_DIR}"
mkdir -p "$(dirname "${OUTPUT_CSV}")"
export HF_HOME
export PYTHONPATH="${PROJECT_DIR}/model:${PYTHONPATH:-}"
export INPUT_CSV
export OUTPUT_CSV
export OFFLINE
export PYTHONFAULTHANDLER=1
if [[ "${OFFLINE}" == "1" ]]; then
export HF_HUB_OFFLINE=1
export TRANSFORMERS_OFFLINE=1
fi
if [[ -n "${CONDA_ENV}" ]] && command -v conda >/dev/null 2>&1; then
# shellcheck disable=SC1091
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate "${CONDA_ENV}"
fi
python - <<'PY'
import os
import pandas as pd
import torch
from tqdm import tqdm
from transformers import AutoTokenizer, BigBirdForMaskedLM
from CodonTransformer.CodonPrediction import predict_dna_sequence
input_csv = os.environ["INPUT_CSV"]
output_csv = os.environ["OUTPUT_CSV"]
local_files_only = os.environ.get("OFFLINE", "1") == "1"
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
print(f"HF_HOME: {os.environ.get('HF_HOME')}")
print(f"Device: {device}")
print(f"Local files only: {local_files_only}")
print(f"Input CSV: {input_csv}")
tokenizer = AutoTokenizer.from_pretrained(
"adibvafa/CodonTransformer",
local_files_only=local_files_only,
)
model = BigBirdForMaskedLM.from_pretrained(
"adibvafa/CodonTransformer",
local_files_only=local_files_only,
).to(device)
dataset = pd.read_csv(input_csv)
if "Unnamed: 0" in dataset.columns:
dataset = dataset.drop(columns=["Unnamed: 0"])
required_columns = {"protein_sequence", "organism"}
missing = required_columns - set(dataset.columns)
if missing:
raise ValueError(f"Input CSV is missing required columns: {sorted(missing)}")
dataset["predicted_dna"] = ""
for index, row in tqdm(dataset.iterrows(), total=len(dataset), desc="Predicting"):
output = predict_dna_sequence(
protein=row["protein_sequence"],
organism=row["organism"],
device=device,
tokenizer=tokenizer,
model=model,
attention_type="original_full",
deterministic=True,
)
dataset.loc[index, "predicted_dna"] = output.predicted_dna
dataset.to_csv(output_csv, index=False)
print(f"Saved predictions to {output_csv}")
PY
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