Domain2GO.py

import streamlit as st
import streamlit.components.v1 as components
import requests
from io import StringIO
from Bio import SeqIO
import os
import time
import pandas as pd

from run_domain2go_app import *


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


with st.sidebar:
    st.title("Domain2GO: Mutual Annotation-Based Prediction of Protein Domain Functions")
    st.write("[![biorxiv](https://img.shields.io/badge/bioRxiv-2022.11.03.514980-b31b1b.svg)](https://www.biorxiv.org/content/10.1101/2022.11.03.514980v1) [![github-repository](https://img.shields.io/badge/GitHub-black?logo=github)](https://github.com/HUBioDataLab/Domain2GO)")

    if 'example_seq_button' not in st.session_state:
        st.session_state.example_seq_button = False

    def click_button():
        st.session_state.example_seq_button = not st.session_state.example_seq_button
    
    input_type = st.radio('Select input type', ['Enter sequence', 'Upload FASTA file'])
    if input_type == 'Enter sequence':
        if st.session_state.example_seq_button:
            st.session_state['sequence'] = st.text_area('Enter protein sequence in FASTA format.', 
                value='>sp|O18783|PLMN_NOTEU\n'
                'MEYGKVIFLFLLFLKSGQGESLENYIKTEGASLSNSQKKQFVASSTEECEALCEKETEFVCRSFEHYNKEQKCVIMSENSKTSSVERKRDVVLFEKRIYLSDCKSGNGRNYRGTLSKTKSGITCQKWSDLSPHVPNYAPSKYPDAGLEKNYCRNPDDDVKGPWCYTTNPDIRYEYCDVPECEDECMHCSGENYRGTISKTESGIECQPWDSQEPHSHEYIPSKFPSKDLKENYCRNPDGEPRPWCFTSNPEKRWEFCNIPRCSSPPPPPGPMLQCLKGRGENYRGKIAVTKSGHTCQRWNKQTPHKHNRTPENFPCRGLDENYCRNPDGELEPWCYTTNPDVRQEYCAIPSCGTSSPHTDRVEQSPVIQECYEGKGENYRGTTSTTISGKKCQAWSSMTPHQHKKTPDNFPNADLIRNYCRNPDGDKSPWCYTMDPTVRWEFCNLEKCSGTGSTVLNAQTTRVPSVDTTSHPESDCMYGSGKDYRGKRSTTVTGTLCQAWTAQEPHRHTIFTPDTYPRAGLEENYCRNPDGDPNGPWCYTTNPKKLFDYCDIPQCVSPSSFDCGKPRVEPQKCPGRIVGGCYAQPHSWPWQISLRTRFGEHFCGGTLIAPQWVLTAAHCLERSQWPGAYKVILGLHREVNPESYSQEIGVSRLFKGPLAADIALLKLNRPAAINDKVIPACLPSQDFMVPDRTLCHVTGWGDTQGTSPRGLLKQASLPVIDNRVCNRHEYLNGRVKSTELCAGHLVGRGDSCQGDSGGPLICFEDDKYVLQGVTSWGLGCARPNKPGVYVRVSRYISWIEDVMKNN')
        else:
            st.session_state['sequence'] = st.text_input('Enter protein sequence in FASTA format.')
        st.session_state['name'] = st.session_state['sequence'].split('\n')[0].strip('>')
        st.button('Use example sequence', on_click=click_button)
    else:
        protein_input = st.file_uploader('Choose file')
        if protein_input:
            protein_input_stringio = StringIO(protein_input.getvalue().decode("utf-8"))
            fasta_sequences = SeqIO.parse(protein_input_stringio, 'fasta')
            for fasta in fasta_sequences:
                st.session_state['name'], st.session_state['sequence'] = fasta.id, str(fasta.seq)

    st.session_state['email'] = st.text_input('Enter your email for InterProScan query*: ')
    st.markdown("""
    <p style="color:#000000;font-size:12px;">*InterProScan requests your email to notify you when your job is done. Your email will not be used for any other purpose.</p>
    """, unsafe_allow_html=True)

# prevent user from clicking submit button if email or sequence is empty
submitted = False


with st.sidebar:
    if st.button('Predict functions'):
        if 'email' in st.session_state and 'sequence' in st.session_state and '@' in st.session_state.email:
            submitted = True
            st.session_state.disabled = True
        else:
            with st.sidebar:
                st.warning('Please enter your email and protein sequence first. If you have already entered your email and protein sequence, please check that your email is valid.')

with st.sidebar:
    c = st.container()
    c.markdown("---")
    c.markdown(
        """
        <div style="padding:5px">
        <p style="color:#000000;font-size:12px;">Disclaimer: This program is designed to generate predictions for a single protein due to the extended runtime of InterProScan. If you need predictions for multiple UniProtKB/Swiss-Prot proteins, we recommend utilizing our comprehensive protein function prediction dataset available in our <a href="https://github.com/HUBioDataLab/Domain2GO">Github repository</a>.</p>
        </div>
        """, unsafe_allow_html=True)
    
if not submitted:
    # on main page, write warning message if user has not submitted email and sequence
    st.markdown("""
    <div style="padding:30px">
    <p style="color:#2a7b36;font-size:20px;">Submit your protein sequence to start.</p>
    </div>
    """, unsafe_allow_html=True)

no_domains = False
error_in_interproscan = False
if submitted:
    with st.spinner('Finding domains in sequence using InterProScan. This may take a while...'):
        result = find_domains(st.session_state.email, st.session_state.sequence, st.session_state.name)
    result_text = result[0]
    if result_text == 'Domains found.':
        # st.success(result_text + ' You can now see function predictions for the sequence in the "Function predictions" tab.')
        st.session_state['domain_df'] = result[1]
    elif result_text == 'No domains found.':
        st.warning(result_text)
        no_domains = True
    else:
        st.error(result_text)
        st.write(f'InterProScan job id: {result[1]}')
        st.write(f'InterProScan job response: {result[2]}')
        error_in_interproscan = True


# if 'domain_df' in st.session_state:
#     with st.expander('Show domains in sequence'):
#         st.write(st.session_state.domain_df)
#         domains_csv = convert_df(st.session_state.domain_df)
#         st.download_button(
#             label="Download domains in sequence as CSV",
#             data=domains_csv,
#             file_name=f"{st.session_state.name}_domains.csv",
#             mime="text/csv",
#         )

if 'domain_df' not in st.session_state:
    if error_in_interproscan:
        st.error('Error in InterProScan. Please check InterProScan job id and response.')
else:
    with st.spinner('Generating function predictions...'):
        cwd = os.getcwd()
        # mapping_path = "{}/Domain2GO/data".format(cwd.split("Domain2GO")[0])
        mapping_path = './data'
        pred_results = generate_function_predictions(st.session_state.domain_df, mapping_path)
        pred_result_text = pred_results[0]
        if pred_result_text == 'Function predictions found.':
            st.success('Function predictions generated.')
            st.session_state['pred_df'] = pred_results[1]
        elif pred_result_text == 'No predictions made for domains found in sequence.':
            st.warning(pred_result_text)

    if 'pred_df' in st.session_state:
        with st.expander('Show function predictions'):
            st.write(st.session_state.pred_df)
            pred_csv = convert_df(st.session_state.pred_df)
            st.download_button(
                label="Download function predictions as CSV",
                data=pred_csv,
                file_name=f"{st.session_state.name}_function_predictions.csv",
                mime="text/csv",
            )