app.py

import gradio as gr
import torch
from pathlib import Path
from helpers import load_model, parse_fasta_string
from io import StringIO
import csv
import tempfile
import transformers
# mute esm warning for weights
transformers.logging.set_verbosity_error()

# Constants
MODEL_NAME = "esm2_t33_650M_UR50D"
CURRENT_DIR = Path(__file__).parent
PATH_MODEL = CURRENT_DIR / "model"
DEVICE = "cpu"
# DEVICE = torch.device('cuda' if torch.cuda.is_available() else 'cpu') # arount 2 mins for fireprot
VALID_AMINO_ACIDS = set("ACDEFGHIKLMNPQRSTVWY")

model, tokenizer = load_model(MODEL_NAME, PATH_MODEL, DEVICE)

def predict_tm(seq_text, seq_file, threshold):
    if seq_file is not None:
        with open(seq_file.name, "r", encoding="utf-8") as f:
            fasta_str = f.read()
    elif seq_text.strip():
        fasta_str = seq_text
    else:
        return "Please provide a sequence via text or file."

    try:
        records = parse_fasta_string(fasta_str)
    except Exception as e:
        return f"FASTA parsing failed: {str(e)}"

    if not records:
        return "No valid sequences found."
    
    results = []
    for i, record in enumerate(records, 1):
        seq = record["sequence"].upper()
        if len(seq) < 20:
            return f"Sequence '{record['id']}' is too short (<20 amino acids)."
        if len(seq) > 2000:
            return f"Sequence '{record['id']}' is too long (>2000 amino acids)."

        if not set(seq).issubset(VALID_AMINO_ACIDS):
            invalid = "".join(set(seq) - VALID_AMINO_ACIDS)
            return f"Invalid characters in sequence: {invalid}"
        inputs = tokenizer(seq, return_tensors="pt", max_length=512, truncation=True, padding=True)
        inputs = {k: v.to(DEVICE) for k, v in inputs.items()}
        with torch.no_grad():
            outputs = model(**inputs)
            prediction = outputs.logits.squeeze().item()
        results.append({"id": record["id"], "tm": round(prediction, 2)})
    results_sorted = sorted(results, key=lambda x: x["tm"], reverse=True)
    table = [
        [i + 1, r["id"], r["tm"], "Yes" if r["tm"] > float(threshold) else "No"]
        for i, r in enumerate(results_sorted)
    ]
    csv_buffer = StringIO()
    writer = csv.writer(csv_buffer)
    writer.writerow(["Rank", "ID", "Predicted Tm [°C]", f"Thermostable"])
    writer.writerows(table)
    csv_str = csv_buffer.getvalue()
    with tempfile.NamedTemporaryFile(delete=False, suffix=".csv", mode="w", encoding="utf-8") as tmp:
        tmp.write(csv_str)
        tmp_path = tmp.name
    return table, tmp_path

demo = gr.Blocks(theme=gr.themes.Origin())
with demo:
    with gr.Row():
        with gr.Column(scale=1):
            gr.Image("assets/TmProt_logo.png", width=100, height=100, show_label=False, show_download_button=False, container=False, show_share_button=False, show_fullscreen_button=False, interactive=False)
        with gr.Column(scale=7):
            gr.Markdown("""
                        # TmProt
                        ## Protein Thermostability Predictor
                        """)
            gr.Markdown(value="""
                        ### TmProt is a machine-learning-based protein thermostability predictor that leverages a fine-tuned ESM-2 protein language model to estimate melting temperatures (Tm) of protein sequences. It enables users to upload protein sequences in FASTA format (either pasted as text or uploaded as a file), and outputs predicted Tm values ranked by a user-defined thermostability threshold.
                        
                        **Paper:** [https://doi.org/10.64898/2026.05.07.723192](https://doi.org/10.64898/2026.05.07.723192)  
                        **GitHub:** [https://github.com/loschmidt/TmProt](https://github.com/loschmidt/TmProt)
                        """
                        )
            
        with gr.Column(scale=1):
            gr.Image("assets/logo.png", width=100, height=100, show_label=False, show_download_button=False, container=False, show_share_button=False, show_fullscreen_button=False, interactive=False)
    with gr.Row():
        with gr.Column(scale=4):
            seq_text = gr.Textbox(
                label="FASTA sequences",
                lines=6,
                placeholder=">seq\nMKTIIALSYIFCLVFA",
                value="",
            )
            seq_file = gr.File(label="Or upload FASTA file", file_types=[".fasta", ".fa", ".txt"], type="filepath")
            btn = gr.Button("Predict")
            cutoff_bins = [str(x) for x in range(20, 101, 10)]
            cutoff_bar = gr.Radio(
                choices=cutoff_bins,
                label="Select thermostability threshold (°C)",
                info="Default is 60°C",
                value="60"
            )
        with gr.Column(scale=4):
            output = gr.Dataframe(headers=["Rank", "ID", "Predicted Tm [°C]", "Thermostable"], label="Results")
            download_btn = gr.DownloadButton(label="Download CSV")
    btn.click(
        predict_tm,
        inputs=[seq_text, seq_file, cutoff_bar],
        outputs=[output, download_btn]
    )
    with gr.Row():
        gr.Examples(
            examples = [
            [""">I1W5V5
MSIENLSSNKSFGGWHKQYSHVSNTLNCAMRFAIYLPPQASTGAKVPVLYWLSGLTCSDENFMQKAGAQRLAAELGIAIVAPDTSPRGEGVADDEGYDLGQGAGFYVNATQAPWNRHYQMYDYVVNELPELIESMFPVSDKRAIAGHSMGGHGALTIALRNPERYQSVSAFSPINNPVNCPWGQKAFTAYLGKDTDTWREYDASLLMRAAKQYVPALVDQGEADNFLAEQLKPEVLEAAASSNNYPLELRSHEGYDHSYYFIASFIEDHLRFHSNYLNA
             """,
                        None,           # seq_file is None (we use text)
                        "60"            # threshold
                    ],
                    [  
             """>R4YJ85
MINLEKALAGRRILIVDDLVEARSSLKKMATILGGDNIDVATDGIEAMSLIHEHEYDIVLSDYNLGRTKDGQQILEEARFTQRLRATSLFIVITGENAIDMVMGALEYDPDGYITKPYTLNMLKERLIRIITIKEELRKVNKAIDLQKYDLAIKYCLEVLDSNPRLRLPASRILGQLLMRQKRFQQALKIYSQLLNERSVSWAKLGQAICIFKLGDPNSALALLNRALVDHPLYVQCYDWIAKILLTLDKPLEAQAALEKAIVISPKAVLRQMELGRIAYENGDMVTAEPAFKYSVRLGRFSCHKSAKNYLQFVRSAQALLINPKERQTQNKANEAFRALTELKQDFSDDKDSLFEASIVESKTHLKMENLDEAKRSANDAEDMLAKLECPKIDYKLQMTETFIETDQSVKAQKMIDELKSAELSDKQIIMLNRLDNDLNGEALKRHSTSLNDQGVSHYEKGELEEAIIAFDQATHYEQAGISVLLNSIQAKISLMERDSPDKKILKNVRSLLIRIGEIAKDDERFARYSRLRKTYDRLCRAAAK
             """,
                        None,
                        "50"
                    ],
            ],
            inputs=[seq_text, seq_file, cutoff_bar],
            label="Click an example to try TmProt instantly",
            examples_per_page=2,
        )
    with gr.Row():
        with gr.Column(scale=1):
                pass
        with gr.Column(scale=7):
            gr.Markdown(value="""
                ## Features

                    - Predict protein melting temperature (Tm) from amino acid sequences

                    - Accepts input via FASTA text or FASTA file upload

                    - Supports sequences from 20 to 2000 amino acids in length

                    - Outputs a ranked table with predicted Tm and thermostability status based on user-chosen threshold

                    - CSV download option for easy export and downstream analysis

                ## Model Overview

                    - Base Model: facebook/esm2_t33_650M_UR50D (650M parameters)

                    - Fine-tuning method: LoRA (Low-Rank Adaptation) using PEFT framework

                    - Task: Regression prediction of protein melting temperature (Tm)

                    - Training Data: ProMelt dataset (merged Meltome Atlas + ProTherm) with ~45,000 protein sequences and experimental Tm values

                    - Output: Single linear regression output neuron predicting Tm in °C
            """
            )
        with gr.Column(scale=1):
            pass            

if __name__ == "__main__":
    demo.launch(share=True, allowed_paths=['./assets'])