def test_ignore_columns(self):
names = ["gene_id"]
roles = ['feature_id']
for i in range(8):
names.append('sample_' + str(i))
if (i % 2) == 0:
roles.append('sample')
else:
roles.append(None)
schema = Schema(
column_names=names,
column_roles=roles)
self.assertEquals(len(schema.sample_column_names), 4)
schema.add_factor('treated', [False, True])
schema.set_factor('sample_0', 'treated', False)
schema.set_factor('sample_2', 'treated', False)
schema.set_factor('sample_4', 'treated', True)
schema.set_factor('sample_6', 'treated', True)
with self.assertRaises(Exception):
schema.set_factor('sample_1' + str(i), 'treated', True)
self.assertEquals(schema.possible_assignments(['treated']),
[OrderedDict([('treated', False)]),
OrderedDict([('treated', True )])])
self.assertEquals(schema.indexes_with_assignments(
OrderedDict([('treated', False)])),
[0, 1])
self.assertEquals(schema.indexes_with_assignments(
OrderedDict([('treated', True)])),
[2, 3])
self.assertEquals(schema.samples_with_assignments(
OrderedDict([('treated', False)])),
['sample_0', 'sample_2'])
self.assertEquals(schema.samples_with_assignments(
OrderedDict([('treated', True)])),
['sample_4', 'sample_6'])
out = StringIO()
schema.save(out)
loaded = Schema.load(out.getvalue())
out2 = StringIO()
loaded.save(out2)
self.maxDiff = None
self.assertEquals(out.getvalue(),
out2.getvalue())
def test_ignore_columns(self):
names = ["gene_id"]
roles = ['feature_id']
for i in range(8):
names.append('sample_' + str(i))
if (i % 2) == 0:
roles.append('sample')
else:
roles.append(None)
schema = Schema(column_names=names, column_roles=roles)
self.assertEquals(len(schema.sample_column_names), 4)
schema.add_factor('treated', [False, True])
schema.set_factor('sample_0', 'treated', False)
schema.set_factor('sample_2', 'treated', False)
schema.set_factor('sample_4', 'treated', True)
schema.set_factor('sample_6', 'treated', True)
with self.assertRaises(Exception):
schema.set_factor('sample_1' + str(i), 'treated', True)
self.assertEquals(schema.possible_assignments(['treated']), [
OrderedDict([('treated', False)]),
OrderedDict([('treated', True)])
])
self.assertEquals(
schema.indexes_with_assignments(OrderedDict([('treated', False)])),
[0, 1])
self.assertEquals(
schema.indexes_with_assignments(OrderedDict([('treated', True)])),
[2, 3])
self.assertEquals(
schema.samples_with_assignments(OrderedDict([('treated', False)])),
['sample_0', 'sample_2'])
self.assertEquals(
schema.samples_with_assignments(OrderedDict([('treated', True)])),
['sample_4', 'sample_6'])
out = StringIO()
schema.save(out)
loaded = Schema.load(out.getvalue())
out2 = StringIO()
loaded.save(out2)
self.maxDiff = None
self.assertEquals(out.getvalue(), out2.getvalue())
def test_yaml(self):
self.maxDiff = None
# Save the schema, load it, and save it again. Compare the two
# versions to make sure they're the same, so that we know we
# can round-trip.
out = StringIO()
self.schema.save(out)
loaded = Schema.load(out.getvalue())
out2 = StringIO()
loaded.save(out2)
self.assertEquals(out.getvalue(), out2.getvalue())
def test_yaml(self):
self.maxDiff = None
# Save the schema, load it, and save it again. Compare the two
# versions to make sure they're the same, so that we know we
# can round-trip.
out = StringIO()
self.schema.save(out)
loaded = Schema.load(out.getvalue())
out2 = StringIO()
loaded.save(out2)
self.assertEquals(out.getvalue(),
out2.getvalue())
def load_schema(db):
schema_str = StringIO(db.attrs['schema'])
return Schema.load(schema_str)
def load_schema(path):
try:
with open(path) as f:
return Schema.load(f)
except IOError as e:
raise UsageException("Couldn't load schema: " + e.filename + ": " + e.strerror)
def load_schema(db):
schema_str = StringIO(db.attrs['schema'])
return Schema.load(schema_str)
def load(self):
with open(self.path) as f:
return Schema.load(f)
def load(self):
with open(self.path) as f:
return Schema.load(f)
