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tisigner.py
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tisigner.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon May 20 10:36:23 2019
@author: bikash
"""
import os
from multiprocessing import Pool
from flask import Flask
from flask import request
from flask import send_from_directory
from flask import make_response
from flask import jsonify
from flask_cors import CORS
from flask import send_file
import pandas as pd
import numpy as np
import functions
from functions import Optimiser
from razor import RAZOR
import data
import io
app = Flask(__name__, static_folder='build')
cors = CORS(app)
@app.route('/optimise', methods=["POST"])
def optimiser():
'''Optimisation
'''
try:
seq, ncodons = functions.parse_input_sequence(request.json)
utr = functions.parse_input_utr(request.json)
host = functions.parse_hosts(request.json)
niter, num_seq = functions.parse_algorithm_settings(request.json)
rms = functions.parse_input_rms(request.json)
if utr == data.pET21_UTR and host == 'ecoli':
threshold = functions.parse_fine_tune(request.json)
else:
threshold = None
termcheck = functions.parse_term_check(request.json)
seed = functions.parse_seed(request.json)
if request.json.get('optimisationDirection'):
direction = request.json.get('optimisationDirection')
else:
direction = 'increase-accessibility'
seeds = list(range(seed, seed+num_seq))
rand_states = [np.random.RandomState(i) for i in seeds]
new_opt = Optimiser(seq=seq, host=host, ncodons=ncodons, utr=utr, \
niter=niter, threshold=threshold, \
rms_sites=rms, direction=direction)
pools = Pool(num_seq)
results = []
for result in pools.imap(new_opt.simulated_anneal,\
rand_states):
results.append(result)
pools.close()
pools.join()
result_df = functions.sort_results(functions.sa_results_parse(results,\
threshold=threshold, \
termcheck=termcheck),\
direction=direction, termcheck=termcheck)
json_data = result_df.groupby(['Type', 'Sequence'], sort=False).apply(lambda x:\
functions.send_data(x, utr=utr,
host=host)).groupby(level=0).\
apply(lambda x: x.tolist()).to_json(\
orient='columns')
return json_data
except Exception as exp:
if 'pools' in locals():
pools.close()
pools.join()
return make_response(jsonify({'data':str(exp), 'status':500}), 500)
@app.route('/razor', methods=['POST'])
def razor_predict():
try:
seq, max_scan = functions.parse_input_razor(request.json)
# print(seq, max_scan)
newObj = RAZOR(seq=seq, max_scan=max_scan)
_ = newObj.predict()
try:
_ = newObj.fungi()
_ = newObj.toxin()
except TypeError:
pass
try:
cleav = newObj.final_cleavage.tolist()[0]
except Exception:
cleav = 0
response_dict = {
'y_score':np.around(newObj.y_scores, 2).tolist(),
'all_probs':newObj.cs_probs_all.tolist(),
'predictions':newObj.preds.tolist(),
'cleavage':cleav,
'final_score_sp':np.around(newObj.final_score_sp, 2),
'final_cleavage_prob':newObj.final_cleavage_prob,
'fungi_scores':newObj.fungi_scores.tolist(),
'fungi_preds':newObj.fungi_preds.tolist(),
'final_score_fungi':newObj.final_score_fungi,
'toxin_scores':newObj.toxin_scores.tolist(),
'toxin_preds':newObj.toxin_preds.tolist(),
'final_score_toxin':newObj.final_score_toxin,
}
return make_response(jsonify(response_dict), 200)
except Exception as exp:
return make_response(jsonify({'data':str(exp), }), 500)
@app.route('/interactions', methods=["POST"])
def scallion_web():
try:
file = request.json.get('inputSequenceScallion').\
upper()
df = functions.fasta_reader(io.StringIO(file))
res = functions.scallion(df).to_csv(index=False)
return make_response(jsonify(res), 200)
except Exception as exp:
return make_response(jsonify({'data':str(exp), }), 500)
# Serve React App
@app.route('/', defaults={'path': ''})
@app.route('/<path:path>')
def serve(path):
if path != "" and os.path.exists(app.static_folder + '/' + path):
return send_from_directory(app.static_folder, path)
else:
return send_from_directory(app.static_folder, 'index.html')
if __name__ == '__main__':
app.run(host='0.0.0.0', port='5050', threaded=True, debug=False)