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| from tempfile import NamedTemporaryFile | |
| from gradio import Blocks, Button, Checkbox, Dropdown, Examples, File, HTML, Markdown, Textbox | |
| from model import get_models | |
| from data import Data | |
| # Define scoring strategies | |
| SCORING = ["wt-marginals", "masked-marginals"] | |
| # Get available models | |
| MODELS = get_models() | |
| def app(*argv): | |
| """ | |
| Main application function | |
| """ | |
| # Unpack the arguments | |
| seq, trg, model_name, *_ = argv | |
| scoring = SCORING[scoring_strategy.value] | |
| try: | |
| # Calculate the data based on the input parameters | |
| data = Data(seq, trg, model_name, scoring, out_file).calculate() | |
| except Exception as e: | |
| # If an error occurs, return an HTML error message | |
| return f'<!DOCTYPE html><html><body><h1 style="background-color:#F70D1A;text-align:center;">Error: {str(e)}</h1></body></html>', None | |
| # If no error occurs, return the calculated data | |
| return repr(data), File(value=out_file.name, visible=True) | |
| # Create the Gradio interface | |
| with open("instructions.md", "r", encoding="utf-8") as md,\ | |
| NamedTemporaryFile(mode='w+') as out_file,\ | |
| Blocks() as esm_scan: | |
| # Define the interface components | |
| Markdown(md.read()) | |
| seq = Textbox( | |
| lines=2, | |
| label="Sequence", | |
| placeholder="FASTA sequence here...", | |
| value='' | |
| ) | |
| trg = Textbox( | |
| lines=1, | |
| label="Substitutions", | |
| placeholder="Substitutions here...", | |
| value="" | |
| ) | |
| model_name = Dropdown(MODELS, label="Model", value="facebook/esm2_t30_150M_UR50D") | |
| scoring_strategy = Checkbox(value=True, label="Use masked-marginals scoring") | |
| btn = Button(value="Run") | |
| out = HTML() | |
| bto = File( | |
| value=out_file.name, | |
| visible=False, | |
| label="Download", | |
| file_count='single', | |
| interactive=False | |
| ) | |
| btn.click( | |
| fn=app, | |
| inputs=[seq, trg, model_name], | |
| outputs=[out, bto] | |
| ) | |
| ex = Examples( | |
| examples=[ | |
| [ | |
| "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ", | |
| "deep mutational scanning", | |
| "facebook/esm2_t6_8M_UR50D" | |
| ], | |
| [ | |
| "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ", | |
| "217 218 219", | |
| "facebook/esm2_t12_35M_UR50D" | |
| ], | |
| [ | |
| "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ", | |
| "R218K R218S R218N R218A R218V R218D", | |
| "facebook/esm2_t30_150M_UR50D", | |
| ], | |
| [ | |
| "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ", | |
| "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMWGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ", | |
| "facebook/esm2_t33_650M_UR50D", | |
| ], | |
| ], | |
| inputs=[seq, | |
| trg, | |
| model_name], | |
| outputs=[out, | |
| bto], | |
| fn=app | |
| ) | |
| # Launch the Gradio interface | |
| if __name__ == "__main__": | |
| esm_scan.launch() | |