def singleThermo(sbml_paths,
pathway_id,
tmpOutputFolder,
ph=7.0,
ionic_strength=200,
pMg=10.0,
temp_k=298.15,
stdev_factor=1.96):
"""Given a list of rpSBML input files, perform thermodynamics analysis. Less memory effecient than the _hdd method but faster
:param sbml_paths: The list of rpSBML paths passed to calculate thermodynamics
:param pathway_id: The id of the heterologous pathway of interest
:param tmpOutputFolder: The path to the output folder to write the result rpSBML file
:param ph: The pH of the host organism (Default: 7.0)
:param ionic_strength: Ionic strenght of the host organism (Default: 200.0)
:param pMg: The pMg of the host organism (Default: 10.0)
:param temp_k: The temperature of the host organism in Kelvin (Default: 298.15)
:param stdev_factor: The standard deviation factor to calculate MDF (Default: 1.96)
:type sbml_paths: str
:type pathway_id: str
:type tmpOutputFolder: str
:type ph: float
:type ionic_strength: float
:type pMg: float
:type temp_k: float
:type stdev_factor: float
:rtype: bool
:return: Success or failure of the function
"""
rpequilibrator = rpEquilibrator.rpEquilibrator(
ph=ph,
ionic_strength=ionic_strength,
pMg=pMg,
temp_k=temp_k,
stdev_factor=stdev_factor)
for sbml_path in sbml_paths:
logging.debug('Calculating the thermodynamics of the pathway ' +
str(pathway_id) + ' for the file: ' + str(sbml_path))
file_name = sbml_path.split('/')[-1].replace('.sbml', '').replace(
'.xml', '').replace('.rpsbml', '').replace('_rpsbml', '')
rpsbml = rpSBML.rpSBML(file_name, path=sbml_path)
rpequilibrator.rpsbml = rpsbml
res = rpequilibrator.pathway(
pathway_id, True) #ignore the results because written in SBML file
rpsbml.writeSBML(tmpOutputFolder)
rpsbml = None
return True
def runEqSBtab_hdd(inputTar,
outputTar,
pathway_id='rp_pathway',
fba_id=None,
thermo_id='dfG_prime_o',
ph=7.0,
ionic_strength=200,
pMg=10.0,
temp_k=298.15,
stdev_factor=1.96):
"""Given a tar input file, perform MDF analysis for each rpSBML file.
:param inputTar: The path to the input TAR file
:param outputTar: The path to the output TAR file
:param pathway_id: The id of the heterologous pathway of interest (Default: rp_pathway)
:param fba_id: The id of the FBA value. Default sets all FBA values to 1.0 and if specified (Default: None)
:param thermo_id: The id of the thermodynamics id (Default: dfG_prime_o)
:param ph: The pH of the host organism (Default: 7.0)
:param ionic_strength: Ionic strenght of the host organism (Default: 200.0)
:param pMg: The pMg of the host organism (Default: 10.0)
:param temp_k: The temperature of the host organism in Kelvin (Default: 298.15)
:param stdev_factor: The standard deviation factor to calculate MDF (Default: 1.96)
:type inputTar: str
:type outputTar: str
:type pathway_id: str
:type tmpOutputFolder: str
:type ph: float
:type ionic_strength: float
:type pMg: float
:type temp_k: float
:type stdev_factor: float
:rtype: bool
:return: Success or failure of the function
"""
rpequilibrator = rpEquilibrator.rpEquilibrator(
ph=ph, ionic_strength=ionic_strength, pMg=pMg, temp_k=temp_k)
with tempfile.TemporaryDirectory() as tmpInputFolder:
with tempfile.TemporaryDirectory() as tmpOutputFolder:
tar = tarfile.open(inputTar, mode='r')
tar.extractall(path=tmpInputFolder)
tar.close()
if len(glob.glob(tmpInputFolder + '/*')) == 0:
logging.error('Input file is empty')
return False
for sbml_path in glob.glob(tmpInputFolder + '/*'):
logging.debug('=========== ' + str(sbml_path) +
' ============')
fileName = sbml_path.split('/')[-1].replace(
'.sbml',
'').replace('.xml', '').replace('.rpsbml',
'').replace('_rpsbml', '')
rpsbml = rpSBML.rpSBML(fileName, path=sbml_path)
rpequilibrator.rpsbml = rpsbml
status = rpequilibrator.toNetworkSBtab(
os.path.join(tmpOutputFolder, fileName + '.tsv'),
pathway_id, thermo_id, fba_id, stdev_factor)
rpsbml = None
if len(glob.glob(tmpOutputFolder + '/*')) == 0:
logging.error('rpThermo has not produced any results')
return False
with tarfile.open(outputTar, mode='w:gz') as ot:
for sbml_path in glob.glob(tmpOutputFolder + '/*'):
fileName = str(sbml_path.split('/')[-1])
info = tarfile.TarInfo(fileName)
info.size = os.path.getsize(sbml_path)
ot.addfile(tarinfo=info, fileobj=open(sbml_path, 'rb'))
return True
def test_MDF(self):
rpsbml = rpSBML.rpSBML('test',
path=os.path.join('data', 'rpsbml_pathway.xml'))
rpeq = rpEquilibrator.rpEquilibrator(rpsbml)
mdf = rpeq.MDF()
self.assertAlmostEqual(mdf, 205.53445861091302)
def runThermo_hdd(inputTar,
outputTar,
pathway_id='rp_pathway',
ph=7.0,
ionic_strength=200,
pMg=10.0,
temp_k=298.15):
"""Given a tar input file, perform thermodynamics analysis for each rpSBML file.
:param inputTar: The path to the input TAR file
:param outputTar: The path to the output TAR file
:param pathway_id: The id of the heterologous pathway of interest
:param ph: The pH of the host organism (Default: 7.0)
:param ionic_strength: Ionic strenght of the host organism (Default: 200.0)
:param pMg: The pMg of the host organism (Default: 10.0)
:param temp_k: The temperature of the host organism in Kelvin (Default: 298.15)
:param stdev_factor: The standard deviation factor to calculate MDF (Default: 1.96)
:type inputTar: str
:type outputTar: str
:type pathway_id: str
:type tmpOutputFolder: str
:type ph: float
:type ionic_strength: float
:type pMg: float
:type temp_k: float
:type stdev_factor: float
:rtype: bool
:return: Success or failure of the function
"""
rpequilibrator = rpEquilibrator.rpEquilibrator(
ph=ph, ionic_strength=ionic_strength, pMg=pMg, temp_k=temp_k)
with tempfile.TemporaryDirectory() as tmpOutputFolder:
with tempfile.TemporaryDirectory() as tmpInputFolder:
tar = tarfile.open(inputTar, mode='r')
tar.extractall(path=tmpInputFolder)
tar.close()
if len(glob.glob(tmpInputFolder + '/*')) == 0:
logging.error('Input file is empty')
return False
for sbml_path in glob.glob(tmpInputFolder + '/*'):
logging.debug('Passing the sbml file: ' + str(sbml_path))
fileName = sbml_path.split('/')[-1].replace(
'.sbml',
'').replace('.xml', '').replace('.rpsbml',
'').replace('_rpsbml', '')
rpsbml = rpSBML.rpSBML(fileName, path=sbml_path)
rpequilibrator.rpsbml = rpsbml
res = rpequilibrator.pathway(
pathway_id,
True) #ignore the results since written to SBML file
rpsbml.writeSBML(tmpOutputFolder)
rpsbml = None
if len(glob.glob(tmpOutputFolder + '/*')) == 0:
logging.error('rpThermo has not produced any results')
return False
with tarfile.open(outputTar, mode='w:gz') as ot:
for sbml_path in glob.glob(tmpOutputFolder + '/*'):
fileName = str(
sbml_path.split('/')[-1].replace('.sbml', '').replace(
'.xml', '').replace('.rpsbml',
'').replace('_rpsbml', ''))
fileName += '.sbml.xml'
info = tarfile.TarInfo(fileName)
info.size = os.path.getsize(sbml_path)
ot.addfile(tarinfo=info, fileobj=open(sbml_path, 'rb'))
return True
def setUpClass(self):
self.rpsbml = rpSBML.rpSBML('test',
path=os.path.join('data', 'rpsbml.xml'))
self.rpeq = rpEquilibrator.rpEquilibrator(self.rpsbml)