exdesi.py

#!python
# Copyright (c) 2014, Sven Thiele <sthiele78@gmail.com>
#
# This file is part of exdesi.
#
# exdesi is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# exdesi is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with iggy.  If not, see <http://www.gnu.org/licenses/>.
# -*- coding: utf-8 -*-
import sys
import argparse
from pyasp.asp import *
from __exdesi__ import query, utils, bioquali

if __name__ == '__main__':

  parser = argparse.ArgumentParser()

  parser.add_argument("networkfiles",
    help="directory of influence graphs in SIF format")

  parser.add_argument("experivarfile",
    help="experimental variables")

  parser.add_argument('--best_set',type=int, default=-1,
    help="compute best set of experiments maximal number of experiments, default is OFF, 0=unlimited")

  parser.add_argument("-x", "--exclude",
    help="exclude experiments described in file EXCLUDE")

  args       = parser.parse_args()
  net_dir    = args.networkfiles
  exp_string = args.experivarfile
  flist      = os.listdir(net_dir)
  NETS       = TermSet()

  print('\nReading',len(flist),'networks from',net_dir,'...',end='\n')
  for f in flist :
    net_string = os.path.join(net_dir,f)
    print ('   reading',net_string,'... ',end='')
    net  = bioquali.readSIFGraph(net_string)
    NETS = TermSet(NETS.union(net))
    print('done.')

  print('\nReading experimental variables',exp_string, '... ',end='')
  mu = bioquali.readExpVar(exp_string)
  print('done.')
  #print(mu)

  if (args.exclude) :
    print('\nReading excluded experiments',args.exclude, '... ',end='')
    exclude = bioquali.readExcludedExp(args.exclude)
    print('done.')
    #print(exclude)
    MU = TermSet(mu.union(exclude))
  else : MU = mu

  print('\nCompute best single experiment ...',end='')
  experiments = query.get_best_single_experiments(NETS, MU)
  print('done.')

  if experiments == [] :
    print("no experiment can distinguish the networks.")
    print("add more readouts or more perturbations.")
  else:
    count = 0
    for e in experiments :
      count = count+1
      print("best single experiment",count,":")
      utils.print_experiment_table(e)

    if args.best_set > -1 :
      max_number_experiments = args.best_set
      print('\nCompute best experiment sets (max experiments = '+str(max_number_experiments)+') ...',end='')
      max_number_experiments = 10
      experiments = query.get_best_experiment_sets(NETS,MU,max_number_experiments)
      print('done.')

      count = 0
      for e in experiments :
        count = count+1
        print("best experiment set",count,":")
        utils.print_experiment_table(e)

  utils.clean_up()