def test_string_conversion(self):
protein = core.Protein("n", "l", "a-b", "+", "anno")
self.assertEqual(str(protein), "l\tn\ta\tb\t+\tanno\n")
# test name is used when no locus tag
protein = core.Protein("n", "no_locus_tag", "a-b", "+", "anno")
self.assertEqual(str(protein), "n\tn\ta\tb\t+\tanno\n")
# test location
protein = core.Protein("n", "no_locus_tag", "abb", "+", "anno")
with self.assertRaises(ValueError) as context:
str(protein)
self.assertTrue(str(context.exception).startswith("Invalid location in Protein"))
protein = core.Protein("n", "no_locus_tag", 123., "+", "anno")
with self.assertRaises(AttributeError) as context:
str(protein)
def test_missing_removed(self):
proteins = {}
for name in "ABDEFH":
proteins[name] = core.Protein(name, "dummylocus", "1-5", "+",
"annotation")
clusters = {
"1":
core.ReferenceCluster("1", "c1", ["A", "B", "C"], "desc", "type",
["tag1"]),
"2":
core.ReferenceCluster("2", "c1", ["D", "E"], "desc", "type",
["tag3"]),
"3":
core.ReferenceCluster("3", "c1", ["F", "G"], "desc", "type",
["tag2"]),
"4":
core.ReferenceCluster("4", "c2", ["H"], "desc", "type", ["tag4"])
}
core.strip_clusters_missing_proteins(clusters, proteins)
assert sorted(clusters) == ["2", "4"]
assert sorted(proteins) == ["D", "E", "H"]
def test_members(self):
protein = core.Protein("n", "no_locus_tag", "a-b", "+", "anno")
protein.locus_tag = "l"
# if this doesn't raise an exception, __slots__ was removed from Protein
with self.assertRaises(AttributeError):
protein.something = 1
