ASCARIS.py

import streamlit as st
import pandas as pd 
from os import path
import sys
import streamlit.components.v1 as components
sys.path.append('code/')
import pdb_featureVector
import alphafold_featureVector
import argparse
from st_aggrid import AgGrid, GridOptionsBuilder, JsCode,GridUpdateMode
import base64
from huggingface_hub import hf_hub_download
import streamlit as st
import gzip

showWarningOnDirectExecution = False

def convert_df(df):
   return df.to_csv(index=False).encode('utf-8')


if 'visibility' not in st.session_state:
    st.session_state['visibility'] = 'visible'
    st.session_state.disabled =  False

original_title = '<p style="font-family:Trebuchet MS; color:#000000; font-size: 25px; font-weight:bold; text-align:center">ASCARIS</p>'
st.markdown(original_title, unsafe_allow_html=True)
original_title = '<p style="font-family:Trebuchet MS; color:#000000; font-size: 25px; font-weight:bold; text-align:center">(Annotation and StruCture-bAsed RepresentatIon of Single amino acid variations)</p>'
st.markdown(original_title, unsafe_allow_html=True)
 
st.write('')
st.write('')
st.write('')
st.write('')

with st.form('mform', clear_on_submit=False):
    source = st.selectbox('Select the protein structure resource (1: PDB-SwissModel-Modbase, 2: AlphaFold)',[1,2])
    #source = 1
    impute = st.selectbox('Missing value imputation (mostly for the cases where the corresponding annotation does not exist in the protein)',[True, False])
    input_data = st.text_input('Enter SAV data points (format: "UniProt/Swiss-Prot human protein accession" – "wild type a.a." – "position on the sequence" – "mutated a.a.").   Example: P04217-E-20-A or O43556-I-40-A,P57737-W-372-A')
            


    parser = argparse.ArgumentParser(description='ASCARIS')
    
    #parser.add_argument('-s', '--source_option',
    #                    help='Selection of input structure data.\n 1: PDB Structures (default), 2: AlphaFold Structures',
    #                    default=1)
    #parser.add_argument('-i', '--input_datapoint',
    #                    help='Input file or query datapoint\n Option 1: Comma-separated list of identifiers (UniProt ID-wt residue-position-mutated residue (e.g. Q9Y4W6-N-432-T or P41180-E-604-K, Q9Y4W6-N-432-T)) \n Option 2: Enter comma-separated file path')
    #
    #parser.add_argument('-impute', '--imputation_state', default='True',
    #                    help='Whether resulting feature vector should be imputed or not. Default True.')
    
    #args = parser.parse_args()
    
    input_set = input_data
    ###mode = 1
    impute = impute
    submitted = st.form_submit_button(label="Submit", help=None, on_click=None, args=None, kwargs=None, type="secondary", disabled=False, use_container_width=False)
    print('*****************************************')
    print('Feature vector generation is in progress. \nPlease check log file for updates..')
    print('*****************************************')
    #mode = int(mode)
    mode = int(source)
    
selected_df = pd.DataFrame()
st.write('The online tool may be slow, especially while processing multiple SAVs. To address this, please consider using the programmatic version at https://github.com/HUBioDataLab/ASCARIS/')
if submitted:
    with st.spinner('In progress...This may take a while...'):
        try:
            if mode == 1:
                # selected_df = pdb_featureVector.pdb(input_set, mode, impute)   
                pass
                
            elif mode == 2:
                selected_df = alphafold_featureVector.alphafold(input_set, mode, impute)
            else:
                selected_df =  pd.DataFrame()

        except:
            selected_df = pd.DataFrame()
            pass

    if selected_df is None:
        st.success('Feature vector failed. Check the log file.')

    else:
        if len(selected_df) != 0 :
            st.write(selected_df)
            st.success('Feature vector is successfully created.')
            csv = convert_df(selected_df)
    
            st.download_button("Press to Download the Feature Vector", csv,f"ASCARIS_SAV_rep_{input_set}.csv","text/csv",key='download-csv')

        else:
            st.success('Feature vector failed. Check the log file.')