AMP-Classifier / app.py
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import gradio as gr
import joblib
import numpy as np
import pandas as pd
from propy import AAComposition, Autocorrelation, CTD, PseudoAAC
from sklearn.preprocessing import MinMaxScaler
model = joblib.load("RF.joblib")
scaler = joblib.load("norm (1).joblib")
selected_features = [
"_SolventAccessibilityC3", "_SecondaryStrC1", "_SecondaryStrC3", "_ChargeC1", "_PolarityC1",
"_NormalizedVDWVC1", "_HydrophobicityC3", "_SecondaryStrT23", "_PolarizabilityD1001",
"_PolarizabilityD2001", "_PolarizabilityD3001", "_SolventAccessibilityD1001",
"_SolventAccessibilityD2001", "_SolventAccessibilityD3001", "_SecondaryStrD1001",
"_SecondaryStrD1075", "_SecondaryStrD2001", "_SecondaryStrD3001", "_ChargeD1001",
"_ChargeD1025", "_ChargeD2001", "_ChargeD3075", "_ChargeD3100", "_PolarityD1001",
"_PolarityD1050", "_PolarityD2001", "_PolarityD3001", "_NormalizedVDWVD1001",
"_NormalizedVDWVD2001", "_NormalizedVDWVD2025", "_NormalizedVDWVD2050", "_NormalizedVDWVD3001",
"_HydrophobicityD1001", "_HydrophobicityD2001", "_HydrophobicityD3001", "_HydrophobicityD3025",
"A", "R", "D", "C", "E", "Q", "H", "I", "M", "P", "Y", "V",
"AR", "AV", "RC", "RL", "RV", "CR", "CC", "CL", "CK", "EE", "EI", "EL",
"HC", "IA", "IL", "IV", "LA", "LC", "LE", "LI", "LT", "LV", "KC", "MA",
"MS", "SC", "TC", "TV", "YC", "VC", "VE", "VL", "VK", "VV",
"MoreauBrotoAuto_FreeEnergy30", "MoranAuto_Hydrophobicity2", "MoranAuto_Hydrophobicity4",
"GearyAuto_Hydrophobicity20", "GearyAuto_Hydrophobicity24", "GearyAuto_Hydrophobicity26",
"GearyAuto_Hydrophobicity27", "GearyAuto_Hydrophobicity28", "GearyAuto_Hydrophobicity29",
"GearyAuto_Hydrophobicity30", "GearyAuto_AvFlexibility22", "GearyAuto_AvFlexibility26",
"GearyAuto_AvFlexibility27", "GearyAuto_AvFlexibility28", "GearyAuto_AvFlexibility29",
"GearyAuto_AvFlexibility30", "GearyAuto_Polarizability22", "GearyAuto_Polarizability24",
"GearyAuto_Polarizability25", "GearyAuto_Polarizability27", "GearyAuto_Polarizability28",
"GearyAuto_Polarizability29", "GearyAuto_Polarizability30", "GearyAuto_FreeEnergy24",
"GearyAuto_FreeEnergy25", "GearyAuto_FreeEnergy30", "GearyAuto_ResidueASA21",
"GearyAuto_ResidueASA22", "GearyAuto_ResidueASA23", "GearyAuto_ResidueASA24",
"GearyAuto_ResidueASA30", "GearyAuto_ResidueVol21", "GearyAuto_ResidueVol24",
"GearyAuto_ResidueVol25", "GearyAuto_ResidueVol26", "GearyAuto_ResidueVol28",
"GearyAuto_ResidueVol29", "GearyAuto_ResidueVol30", "GearyAuto_Steric18",
"GearyAuto_Steric21", "GearyAuto_Steric26", "GearyAuto_Steric27", "GearyAuto_Steric28",
"GearyAuto_Steric29", "GearyAuto_Steric30", "GearyAuto_Mutability23", "GearyAuto_Mutability25",
"GearyAuto_Mutability26", "GearyAuto_Mutability27", "GearyAuto_Mutability28",
"GearyAuto_Mutability29", "GearyAuto_Mutability30", "APAAC1", "APAAC4", "APAAC5",
"APAAC6", "APAAC8", "APAAC9", "APAAC12", "APAAC13", "APAAC15", "APAAC18", "APAAC19",
"APAAC24"
]
def extract_features(sequence):
"""Extract selected features and normalize them."""
all_features = AAComposition.CalculateAADipeptideComposition(sequence)
feature_values = list(all_features.values())
feature_array = np.array(feature_values).reshape(-1, 1)
feature_array = feature_array[: 420] # Ensure we only use 420 features
normalized_features = scaler.transform(feature_array.T)
normalized_features = normalized_features.flatten()
# Select features that match training data
selected_feature_dict = {feature: normalized_features[i] for i, feature in enumerate(selected_features)
if feature in all_features}
selected_feature_df = pd.DataFrame([selected_feature_dict])
selected_feature_array = selected_feature_df.T.to_numpy()
return selected_feature_array
def extract_features(sequence):
"""Extract selected features and normalize them."""
# Extract features from different methods
aa_features = AAComposition.CalculateAADipeptideComposition(sequence)
auto_features = Autocorrelation.CalculateAutoTotal(sequence)
ctd_features = CTD.CalculateCTD(sequence)
pseaac_features = PseudoAAC.GetAPseudoAAC(sequence, lamda=9)
# Combine all extracted features
all_features = {**aa_features, **auto_features, **ctd_features, **pseaac_features}
normalized_features = scaler.transform(all_features.T)
normalized_features = normalized_features.flatten()
# Select features that match training data
selected_feature_dict = {feature: normalized_features[i] for i, feature in enumerate(selected_features)
if feature in all_features}
selected_feature_df = pd.DataFrame([selected_feature_dict])
selected_feature_array = selected_feature_df.T.to_numpy()
return selected_feature_array
def predict(sequence):
"""Predict if the sequence is an AMP or not."""
features = extract_features(sequence)
prediction = model.predict(features)[0]
probabilities = model.predict_proba(features)[0]
prob_amp = probabilities[0]
prob_non_amp = probabilities[1]
return f"{prob_amp * 100:.2f}% chance of being an Antimicrobial Peptide (AMP)" if prediction == 0 else f"{prob_non_amp * 100:.2f}% chance of being Non-AMP"
iface = gr.Interface(
fn=predict,
inputs=gr.Textbox(label="Enter Protein Sequence"),
outputs=gr.Label(label="Prediction"),
title="AMP Classifier",
description="Enter an amino acid sequence to predict whether it's an antimicrobial peptide (AMP) or not."
)
iface.launch(share=True)