app.py

import multiprocessing
import gradio as gr
import torch
from omnigenome import OmniGenomeModelForRNADesign  # Assuming this is where the model class is defined
import RNA  # ViennaRNA library for RNA structure plotting
import tempfile  # For handling temporary files
import os  # For file operations

# Initialize the model for RNA design
model = OmniGenomeModelForRNADesign(model_path="anonymous8/OmniGenome-186M")
model.to("cuda" if torch.cuda.is_available() else "cpu")


# RNA Design function with structure plotting
def design_rna(target_structure):
    if not 0 < len(target_structure) <= 50:
        return "The online demo only supports RNA structures with 1 to 100 characters.", None

    # Run the genetic algorithm to design RNA sequences
    best_sequences = model.run_rna_design(
        structure=target_structure.strip(),
        mutation_ratio=0.5,
        num_population=50,
        num_generation=100
    )

    # Select the best sequence (assuming it's the first one)
    best_sequence = best_sequences[0]

    # Generate the RNA secondary structure plot
    plot_path = plot_rna_structure(best_sequence, target_structure)

    return best_sequence, plot_path


# Function to plot RNA structure and return the path to the SVG image
def plot_rna_structure(sequence, structure):
    # Create a temporary file to save the SVG plot
    with tempfile.NamedTemporaryFile(delete=False, suffix=".svg") as tmpfile:
        plot_path = tmpfile.name

    # Plot RNA structure using ViennaRNA
    RNA.svg_rna_plot(sequence, structure, plot_path)

    return plot_path


# Launch the app
if __name__ == "__main__":
    multiprocessing.set_start_method('spawn', force=True)

    # Gradio Interface with vertical layout
    with gr.Blocks() as iface:
        gr.Markdown("# RNA Design with OmniGenome")
        gr.Markdown(
            "Enter a target RNA secondary structure to generate a designed RNA sequence and visualize its structure. "
            "Please note that the online demo only supports RNA structures with 1 to 50 bases due to computational resource shortage."
            "For larger structures, please run the model locally."
        )
        gr.Markdown("""
        ### Example RNA Structures:
        - `(((((......)))))`
        - `((((((.((((....))))))).)))..........`
        - `((....)).((....))`
        - `.(((((((((((...)))))....)))))).`
        - `..((((((((.....))))((((.....))))))))..`
        """)

        with gr.Column():
            target_structure_input = gr.Textbox(
                label="Target RNA Secondary Structure",
                placeholder="Enter RNA structure here, e.g., (((((......)))))"
            )
            output_sequence = gr.Textbox(label="Designed RNA Sequence")
            output_plot = gr.Image(type="filepath", label="RNA Structure Plot")

        # Defining the function call on input
        submit_button = gr.Button("Submit")
        submit_button.click(
            design_rna,
            inputs=target_structure_input,
            outputs=[output_sequence, output_plot]
        )

    iface.launch()