def test_map00950(self):
system = System()
with open("KEGG/map00950.rea") as handle:
for reaction in Map.parse(handle):
system.add_reaction(reaction)
rxs = system.reactions()
self.assertEqual(len(rxs), 56)
# sort the reaction output by the string names, so that the
# output will be consistent between python versions
rxs.sort(key=lambda x: str(x))
self.assertEqual(
str(rxs[0]),
"(R)-N-Methylcoclaurine + (S)-Coclaurine + NADPH + O2 "
"<=> 2'-Norberbamunine + 2 H2O + NADP")
self.assertEqual(str(rxs[-1]), "Tyramine <=> Dopamine")
def test_map00950(self):
system = System()
with open("KEGG/map00950.rea") as handle:
for reaction in Map.parse(handle):
system.add_reaction(reaction)
rxs = system.reactions()
self.assertEqual(len(rxs), 56)
# sort the reaction output by the string names, so that the
# output will be consistent between python versions
rxs.sort(key=lambda x: str(x))
self.assertEqual(str(rxs[0]),
"(R)-N-Methylcoclaurine + (S)-Coclaurine + NADPH + O2 "
"<=> 2'-Norberbamunine + 2 H2O + NADP")
self.assertEqual(str(rxs[-1]),
"Tyramine <=> Dopamine")
def t_KEGG_Map(testfiles):
"""Tests Bio.KEGG.Map functionality."""
for file in testfiles:
fh = open(os.path.join("KEGG", file))
print "Testing Bio.KEGG.Map on " + file + "\n\n"
reactions = Map.parse(fh)
system = System()
for reaction in reactions:
system.add_reaction(reaction)
# sort the reaction output by the string names, so that the
# output will be consistent between python versions
def str_cmp(first, second):
return cmp(str(first), str(second))
rxs = system.reactions()
rxs.sort(str_cmp)
for x in rxs:
print str(x)
def t_KEGG_Map(testfiles):
"""Tests Bio.KEGG.Map functionality."""
for file in testfiles:
fh = open(os.path.join("KEGG", file))
print "Testing Bio.KEGG.Map on " + file + "\n\n"
reactions = Map.parse(fh)
system = System()
for reaction in reactions:
system.add_reaction(reaction)
# sort the reaction output by the string names, so that the
# output will be consistent between python versions
#def str_cmp(first, second):
# return cmp(str(first), str(second))
rxs = system.reactions()
#sort: key instead of compare function (for py3 support)
# The function str_cmp above can be removed if the
# solution below proves resilient
rxs.sort(key=lambda x:str(x))
for x in rxs:
print str(x)
def t_KEGG_Map(testfiles):
"""Tests Bio.KEGG.Map functionality."""
for file in testfiles:
fh = open(os.path.join("KEGG", file))
print "Testing Bio.KEGG.Map on " + file + "\n\n"
reactions = Map.parse(fh)
system = System()
for reaction in reactions:
system.add_reaction(reaction)
# sort the reaction output by the string names, so that the
# output will be consistent between python versions
#def str_cmp(first, second):
# return cmp(str(first), str(second))
rxs = system.reactions()
#sort: key instead of compare function (for py3 support)
# The function str_cmp above can be removed if the
# solution below proves resilient
rxs.sort(key=lambda x:str(x))
for x in rxs:
print str(x)
fh.close()