105 lines
3.9 KiB
Python
105 lines
3.9 KiB
Python
#-------------------------------------------------------------------------------
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# Name: SIME
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# Purpose: Scaffold-based enumeration method/software to design in-silico macrolide libraries
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#
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# Author: zinph
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#
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# Created: 27/02/2019
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# Copyright: (c) kzphy 2019
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# Licence: <your licence>
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#-------------------------------------------------------------------------------
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import time
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from flask import Flask, render_template, url_for, request
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from werkzeug import secure_filename
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import os
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from SIME import *
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app = Flask(__name__)
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UPLOAD_FOLDER = 'uploads'
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if not os.path.exists(UPLOAD_FOLDER):
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os.makedirs(UPLOAD_FOLDER)
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app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER
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@app.route('/')
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def main_page():
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return render_template('index.html')
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@app.route('/success')
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def success_page(duration):
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return render_template('success.html', duration=duration)
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@app.route('/collect_data',methods=['POST'])
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def collect_data():
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form_data = request.form
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form_files = request.files
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macrolide_core = form_files.get('macrolide_core')
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structural_motifs_file = form_files.get('structural_motifs_file')
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sugars_file = form_files.get('sugars_file')
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#more options
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max_repeat_motifs = int(form_data.get("max_repeat_motifs"))
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minimal_sugars = int(form_data.get("minimal_sugars"))
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library_size = int(form_data.get("library_size"))
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if form_data.get("enumerate_all_SMs"):
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enumerate_all_SMs = form_data.get("enumerate_all_SMs")
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else:
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enumerate_all_SMs = 'no'
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if form_data.get("enumerate_all_sugars"):
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enumerate_all_sugars = form_data.get("enumerate_all_sugars")
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else:
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enumerate_all_sugars = 'no'
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#enumarate_all = form_data["enumerate_all"]
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if macrolide_core:
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filename = secure_filename(macrolide_core.filename)
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macrolide_core.save(os.path.join(app.config["UPLOAD_FOLDER"],filename))
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macrolide_core = open(os.path.join(UPLOAD_FOLDER,filename),'r')
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else:
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macrolide_core = None
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if structural_motifs_file:
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filename = secure_filename(structural_motifs_file.filename)
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structural_motifs_file.save(os.path.join(app.config["UPLOAD_FOLDER"],filename))
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structural_motifs_file =open(os.path.join(UPLOAD_FOLDER,filename),'r')
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else:
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structural_motifs_file = None
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if sugars_file:
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filename = secure_filename(sugars_file.filename)
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sugars_file.save(os.path.join(app.config["UPLOAD_FOLDER"],filename))
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sugars_file = open(os.path.join(UPLOAD_FOLDER,filename),'r')
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else:
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sugars_file = None
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sample = SIME(structural_motifs_file, sugars_file, max_repeat_motifs, minimal_sugars, library_size, enumerate_all_SMs, enumerate_all_sugars)
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if macrolide_core == None:
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with open("Data/ery_core.txt", 'r') as f:
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smile = f.readline()
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else:
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smile = macrolide_core.readline()
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start_time = time.time()
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sample.generate_templates_withExtendersNSugars(smile)
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duration = convert_time(time.time()-start_time)
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return success_page(duration)
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#return form_data, form_files
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def convert_time(second):
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'''
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Convert second to DAY, HOUR, MIN, SEC format. Parameter is second.
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'''
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day = second/86400
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hour = (day - int(day))*24
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minute = (hour - int(hour))*60
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second = round((minute - int(minute))*60,4)
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return(str(int(day)) + ' DAYS: '+ str(int(hour)) + ' HOURS: '+ str(int(minute)) + ' MINUTES: ' + str(second) + ' SECONDS')
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if __name__ == '__main__':
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app.jinja_env.auto_reload = True
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app.config['TEMPLATES_AUTO_RELOAD']=True #forces flask to reload html templates
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app.config['SEND_FILE_MAX_AGE_DEFAULT'] = 0 #prevents browsers from caching static files served by flask, such as js code
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app.run(host='0.0.0.0', debug=True,use_reloader=True)
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#app.run(host='0.0.0.0',use_reloader=True)
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