app.py

import torch
import torch.nn as nn
from transformers import AutoTokenizer,AutoModelForSequenceClassification,AutoConfig
from torchcrf import CRF
import numpy as np
import pandas as pd
import re
from Bio.Seq import Seq
import matplotlib.pyplot as plt 
from collections import OrderedDict	
from transformers import set_seed
import random
import gradio as gr

def setup_seed(seed):
    set_seed(seed)
    torch.manual_seed(seed)
    torch.cuda.manual_seed_all(seed)
    np.random.seed(seed)
    random.seed(seed)
    torch.backends.cudnn.deterministic = True
setup_seed(4)

device = "cpu"
model_checkpoint = "facebook/esm2_t6_8M_UR50D"

config = AutoConfig.from_pretrained(model_checkpoint)
tokenizer = AutoTokenizer.from_pretrained(model_checkpoint)


def conotoxinfinder(files):
    fr=open(files, 'r')
    seqs = []
    for line in fr:
        if not line.startswith('>'):
            line = line.replace('\n','')
            line = line.replace(' ','')
            if line.islower():
                seqs.append(str((Seq(line).translate())))
            else:
                seqs.append(line)

    model = AutoModelForSequenceClassification.from_pretrained(model_checkpoint, num_labels=1)
    model.load_state_dict(torch.load("best_model.pth"))
    model = model.to(device)

    value_all = []
    for i in seqs:
        tokenizer_test = tokenizer(i, return_tensors='pt').to(device)
        with torch.no_grad():
            value = model(**tokenizer_test)
            value_all.append(np.exp(value["logits"][0].item()))

    summary = OrderedDict()
    summary['Seq'] = seqs
    summary['Value'] = value_all
    summary_df = pd.DataFrame(summary)
    summary_df.to_csv('output.csv', index=False)
    return 'output.csv'

with open("conotoxinfinder.md", "r") as f:
    description = f.read()
iface = gr.Interface(fn=conotoxinfinder,
                     title="ConotoxinFinder α7 regression",
                     inputs=["file"
                             ],
                     outputs= "file",
                     description=description
                     )
iface.launch()