-
Notifications
You must be signed in to change notification settings - Fork 2
/
curate_572_sedml.py
131 lines (101 loc) · 4.42 KB
/
curate_572_sedml.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 2 10:07:17 2022
@author: Lucian
"""
import tellurium as te
from biosimulators_utils.combine.io import CombineArchiveWriter
from biosimulators_utils.combine.io import CombineArchiveReader
from biomodels_qc.utils import build_combine_archive
from run_project_on_biosimulations import runProject
import libsedml
import phrasedml
import libsbml
import os
import glob
import sys
#Fill out this information when you pick a new biomodel:
this_biomodel = 572
sedfilename = "Costa2014.sedml"
sbmlfilename = "BIOMD0000000572_url.xml"
#Everything else should be automatic, but feel free to adjust if need be:
biomdstr = str(this_biomodel).zfill(4)
seddir = "final/BIOMD000000" + biomdstr + "/"
sedfile = seddir + sedfilename
omexfile = "omex_files/BIOMD000000" + biomdstr + ".omex"
#Temp dir to store the files as you're working on them (if seddir isn't appropriate):
outdir = biomdstr + "/"
try:
os.mkdir(outdir)
except:
pass
#Fire things off to Biosimulations:
#runProject("BIOMD000000" + biomdstr)
#Using tellurium to run a SED-ML file:
if te.__version__ > "2.2.4":
te.sedml.tesedml.executeSEDML(sedfile, workingDir=seddir, saveOutputs=True, outputDir=outdir)
else:
te.sedml.tesedml.executeSEDML(sedfile, workingDir=seddir)
#Using tellurium to run a Combine Archive:
te.sedml.tesedml.executeCombineArchive(omexfile, saveOutputs=True, outputDir=outdir)
#Using tellurium to get a file out of a Combine Archive:
sedml = te.extractFileFromCombineArchive(omexfile, sedfilename)
sbml = te.extractFileFromCombineArchive(omexfile, sbmlfilename)
#Using biosimulators_utils to extract files from a Combine Archive:
combine_reader = CombineArchiveReader()
combine_reader.run(omexfile, outdir)
#Using biosimulators_utils to write a Combine Archive:
combine_writer = CombineArchiveWriter()
sedml_filenames = glob.glob(os.path.join(outdir, '**', '*.sedml'), recursive=True)
sedml_locations = [os.path.relpath(path, outdir) for path in sedml_filenames]
archive = build_combine_archive(outdir, sedml_locations)
combine_writer.run(archive, outdir, biomdstr + ".omex")
#View the SBML model in Antimony.
#Note that this bit of code changes how the model is structured, but will not change the math. It's just so that it's easier to read.
sbmldoc = libsbml.readSBMLFromString(sbml)
props = libsbml.ConversionProperties()
props.addOption("expandFunctionDefinitions", True)
if sbmldoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS:
print("[Error] Conversion failed...")
sys.exit(1)
r = te.loads(libsbml.writeSBMLToString(sbmldoc))
print("Antimony version of SBML model", sbmlfilename, ":\n")
print(r.getAntimony())
#Manipulating the SED-ML
#Option 1: Use a text editor
# * Run something like the above to find the SED-ML file as it exists so far.
# * Find the bit that needs to be changed and just change it.
# * Then run the sedml through tellurium to see if it worked.
#Option 2: Use libsedml
#Convert the string to a libsedml document:
sed = libsedml.readSedMLFromString(sedml)
#Example manipulation: remove the 'Removal' curve
# for o in range(sed.getNumOutputs()):
# out = sed.getOutput(o)
# if out.getName() == "Figure 3":
# removeIndex = -1
# for c in range(out.getNumCurves()):
# curve = out.getCurve(c)
# if curve.getName() == "[Removal]":
# removeIndex = c
# out.removeCurve(removeIndex)
# libsedml.writeSedMLToFile(sed, outdir + 'new_sed.sedml')
# te.sedml.tesedml.executeSEDML(outdir + "new_sed.sedml", workingDir=outdir)
#Option 3: Use phraSEDML
# Probably should do this when what you need is very very different from what you have
# (i.e. you need steady state or a parameter scan, but have a time course)
# In this case, we need a version of the model with 'Zombie' set to 0.
new_phrasedml = '''
// Set model
no_zombies = model "munz2000.xml" with Zombie = 0
// Simulation
sim = simulate uniform(0, 10, 1000) # sim_id = simulate simulation_type
no_zombie_sim = run sim on no_zombies # task_id = run sim_id on model_id
plot "Figure 2" time vs Susceptible, Zombie
'''
phrasedml.setWorkingDirectory(outdir)
# The following commands only work with model 882, since the phrasedml refers to that model specifically.
# It's just here for reference if you need it.
# sed2 = phrasedml.convertString(new_phrasedml)
# te.saveToFile(outdir + 'sed2.sedml', sed2)
# te.sedml.tesedml.executeSEDML(outdir + "sed2.sedml", workingDir=outdir)