def test_from_full_sbtab(self):
# Happens to be the order in this file.
rxns, fluxes, keqs, bounds = SBtabTools.openMultipleSBtab(
'pathways/test/EMP_glycolysis_full_SBtab.tsv')
path = pathways.ParsedPathway.from_full_sbtab(rxns, fluxes, bounds,
keqs)
path.print_reactions()
def testFromSBtab(self):
ds = SBtabTools.openMultipleSBtab('pathways/test/EMP_glycolysis_full_SBtab.tsv')
bs = Bounds.from_sbtab(ds[-1])
for key in bs.lower_bounds:
lb = bs.GetLowerBound(key)
ub = bs.GetUpperBound(key)
msg = 'bounds for %s lb = %.2g, ub = %.2g' % (key, lb, ub)
self.assertLessEqual(lb, ub, msg=msg)
def from_sbtab(self, sbtab):
"""
read the sbtab file (can be a filename or file handel)
and use it to initialize the Pathway
"""
if type(sbtab) == str:
with open(sbtab, 'r') as sbtabfile:
sbtabs = SBtabTools.openMultipleSBtabFromFile(sbtabfile)
elif type(sbtab) == io.TextIOWrapper:
sbtabs = SBtabTools.openMultipleSBtabFromFile(sbtab)
tdict = dict([(t.getTableInformation()[1].upper(), t) for t in sbtabs])
expected_tnames = [
'REACTION', 'RELATIVEFLUX', 'CONCENTRATIONCONSTRAINT',
'REACTIONCONSTANT'
]
assert set(expected_tnames).issubset(tdict.keys())
sbtabs = [tdict[n] for n in expected_tnames]
return Pathway.from_separate_sbtabs(*sbtabs)
def read_sbtabs(f):
"""Return reactions, fluxes, keqs, bounds."""
sbtabs = SBtabTools.openMultipleSBtabFromFile(f)
tdict = dict([(t.getTableInformation()[1].upper(), t) for t in sbtabs])
expected_tnames = [
'REACTION', 'RELATIVEFLUX', 'REACTIONCONSTANT',
'CONCENTRATIONCONSTRAINT'
]
assert set(expected_tnames).issubset(tdict.keys())
return [tdict[n] for n in expected_tnames]
def testOpenMultipleSBtab(self):
ds = SBtabTools.openMultipleSBtab(
'tests/EMP_glycolysis_full_SBtab.tsv')
self.assertEqual(4, len(ds))
def testOpenMultipleSBtabFromFile(self):
with open('tests/EMP_glycolysis_full_SBtab.tsv') as f:
ds = SBtabTools.openMultipleSBtabFromFile(f)
self.assertEqual(4, len(ds))
def testOpenMultipleSBtab(self):
ds = SBtabTools.openMultipleSBtab(
'pathways/test/EMP_glycolysis_full_SBtab.tsv')
self.assertEqual(3, len(ds))