def test_wrap_with_space_at_80(self):
source_attributes = {"organism": 'abc', "db_xref": "taxon:5678", "note": "chromX"}
feature = EMBLFeature('source', 1, 1234, '+', source_attributes)
formatted_product = feature.product_attribute_formatter('product','Permease for cytosine/purines, uracil, thiamine, allantoin')
expected_product = 'FT /product="Permease for cytosine/purines, uracil, thiamine,\n' + \
'FT allantoin"'
def test_no_wrap_at_length_80(self):
source_attributes = {"organism": 'abc', "db_xref": "taxon:5678", "note": "chromX"}
feature = EMBLFeature('source', 1, 1234, '+', source_attributes)
formatted_product = feature.product_attribute_formatter('product','1,4-dihydroxy-2-naphthoate octaprenyltransferase')
expected_product = 'FT /product="1,4-dihydroxy-2-naphthoate octaprenyltransferase"'
assert len(expected_product) == 80
self.assertEqual(formatted_product, expected_product)
def test_no_wrap_at_length_79(self):
source_attributes = {"organism": 'abc', "db_xref": "taxon:5678", "note": "chromX"}
feature = EMBLFeature('source', 1, 1234, '+', source_attributes)
formatted_product = feature.product_attribute_formatter('product','Anthranilate 1,2-dioxygenase ferredoxin subunit')
expected_product = 'FT /product="Anthranilate 1,2-dioxygenase ferredoxin subunit"'
assert len(expected_product) == 79
self.assertEqual(formatted_product, expected_product)
def test_initializer_for_ignored_features(self):
feature = EMBLFeature(
feature_type='ncRNA',
start = 100,
end = 200,
strand = '+',
feature_attributes = {'some_attribute': 'ABC' }
)
self.assertEqual(feature.format(), None)
def test_split_product_attribute_on_hyphen(self):
source_attributes = {"organism": 'abc', "db_xref": "taxon:5678", "note": "chromX"}
feature = EMBLFeature('source', 1, 1234, '+', source_attributes)
# TODO: This test currently 'passes' but shows the undesirable
# behaviour of splitting up a long word.
formatted_product = feature.product_attribute_formatter('product','2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase')
expected_product = 'FT /product="2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy\n' + \
'FT late synthase"'
self.assertEqual(formatted_product, expected_product)
def test_split_product_attribute_on_hyphen(self):
source_attributes = {"organism": 'abc', "db_xref": "taxon:5678", "note": "chromX"}
feature = EMBLFeature('source', 1, 1234, '+', source_attributes)
formatted_product = feature.product_attribute_formatter('product','2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase')
expected_product = """\
FT /product="2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carbox
FT ylate synthase"
"""
self.assertEqual(formatted_product, expected_product)
def create_uninitialized_feature(self): # In most cases I don't want tests to run the __init__ # This creates an otherwise identical EMBLFeature object return EMBLFeature.__new__(EMBLFeature)