def test_all_optimization_scripts():
"""TODO: To be deprecated or convert to example in Jupyter notebook.
"""
logger = create_logger(name="optstoicpy.test.testAll")
logger.info("Test optstoic")
lp_prob1, pathways1 = optstoic.test_optstoic()
logger.info(
"Test optstoic glycolysis. Runtime depends on the solver used.")
lp_prob2, pathways2 = optstoic_gly.test_optstoic_glycolysis()
logger.info("Generate kegg_model and draw pathway")
res_dir = os.path.join(current_dir, 'result/')
if not os.path.exists(res_dir):
os.makedirs(res_dir)
f = open(os.path.join(res_dir, 'test_KeggModel.txt'), 'w+')
for ind, p in pathways2.items():
p.rearrange_reaction_order()
generate_kegg_model(p, filehandle=f)
graph_title = "{0}_{1}ATP_P{2}".format(p.name, p.nATP, p.id)
drawpathway.draw_pathway(p,
os.path.join(res_dir +
'/pathway_{0:03d}'.format(p.id)),
imageFormat='png',
graphTitle=graph_title)
f.close()
logger.info("optstoicpy.test.testAll completed!")
def runAnalysis(resultDict, numATP, outputFilePath, imgFormat='png', shift_pathway_id_by=0,\
sourceSubstrateID='C00031', endSubstrateID='C00022', darkBackgroundMode=False):
logging.info("Analyzing results... \n")
pathway_objects = []
outputFileName='OptStoic_gams_{0}ATP'.format(numATP)
f = open(os.path.join(outputFilePath, outputFileName + '_KeggModel.txt'), 'w+')
for ind, res in sorted(resultDict.items()):
logging.debug("Pathway %s"%ind)
if "pathway" not in res:
logging.info("OptStoic terminated with infeasible solution.")
continue
elif "num_reaction" not in res:
logging.info("Pathway is incomplete...")
continue
p = Pathway(id=int(ind)+shift_pathway_id_by, name='OptStoic_gams', reaction_ids=list(res['pathway'].keys()),
fluxes=list(res['pathway'].values()), sourceSubstrateID=sourceSubstrateID, endSubstrateID=endSubstrateID,
total_flux_no_exchange=res['total_flux_no_exchange'],
note={'modelstat': res.get("modelstat"), 'solvestat': res.get("solvestat")})
p.rearrange_reaction_order()
pathway_objects.append(p)
generate_kegg_model(p, filehandle=f)
graph_title = "{0}_{1}ATP_P{2}".format(p.name, p.nATP, p.id)
if res['modelstat'] != 1:
graph_title += '; Modelstat={0}'.format(res['modelstat'])
if imgFormat:
draw_pathway(p, os.path.join(outputFilePath+'/pathway_{0:03d}'.format(p.id)),
imageFormat=imgFormat, graphTitle=graph_title, darkBackgroundMode=darkBackgroundMode)
#pickle.dump(resultDict, open(outputFilePath+outputFileName+'_pathways_dict.pkl', 'w+'))
pickle.dump(pathway_objects, open(outputFilePath + outputFileName + '_pathways_obj.pkl', 'w+'))
logging.info("\nDone!\n")
logging.info("Check your output folder: %s"%outputFilePath)
return pathway_objects
def test_kegg_model_generation(self):
self.logger.info(
"Creating 'res' folder in the current directory if not exist...")
# outputFilepath = 'res'
# outputFilename = 'OptStoic'
# try:
# os.makedirs(outputFilepath)
# except OSError:
# if not os.path.isdir(outputFilepath):
# raise Exception
self.logger.info("Test create KEGG model file")
filename = "./test_kegg_model_generation.txt"
f = open(filename, 'a+')
kegg_model_text = generate_kegg_model(self.p1, filehandle=f)
print(kegg_model_text)
self.assertIn('R01512', kegg_model_text)
self.assertIn('R01512', kegg_model_text)
f.close()
if os.path.exists(filename):
os.remove(filename)