#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018 Piero Dalle Pezze
#
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# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# SOFTWARE.
import re
from sbpipe.simul.copasi import copasi as copasi_simul
from sbpipe.simul import pl_simul
[docs]def generic_postproc(infile,
outfile,
sim_length,
copasi=True):
"""
Perform post processing organisation to double parameter scan report files.
:param infile: the model to process
:param outfile: the directory to store the results
:param sim_length: the length of the simulation
:param copasi: True if the model is a Copasi model
"""
# copy file removing empty lines
with open(infile, 'r') as filein, \
open(outfile, 'w') as fileout:
for line in filein:
if not line.isspace():
fileout.write(line)
if copasi:
simulator = copasi_simul.Copasi()
else:
simulator = pl_simul.PLSimul()
simulator.replace_str_in_report(outfile)
# Extract a selected time point from all perturbed time courses contained in the report file
with open(outfile, 'r') as filein:
header = filein.readline()
timepoints = list(range(0, sim_length + 1))
filesout = []
try:
rep = re.findall(r'_\d+.csv', outfile)[0]
filetemplate = outfile.replace(rep, '')
filesout = [open(filetemplate + '__rep' + rep[:-4] + '__tp_%d.csv' % k, 'w') for k in timepoints]
# copy the header
for fileout in filesout:
fileout.write(header)
# extract the i-th time point and copy it to the corresponding i-th file
for line in filein:
tp = line.rstrip().split('\t')[0]
if '.' not in tp and int(tp) in timepoints:
filesout[int(tp)].write(line)
finally:
for fileout in filesout:
fileout.close()
[docs]def ps2_postproc(infile,
outfile,
sim_length,
copasi=True):
"""
Perform post processing organisation to double parameter scan report files.
:param infile: the model to process
:param outfile: the directory to store the results
:param sim_length: the length of the simulation
:param copasi: True if the model is a Copasi model
"""
generic_postproc(infile, outfile, sim_length, copasi)