def test_contains(self):
# empty list
blank = uniprot_kb.UniProtRecordList()
self.assertFalse(uniprot_kb.UniProtRecord() in blank)
self.assertFalse(self.list[0] in blank)
# non-empty list
self.assertFalse(uniprot_kb.UniProtRecord() in self.list)
self.assertTrue(self.list[0] in self.list)
self.assertTrue(copy.copy(self.list[0]) in self.list)
def test_extend(self):
cpy = copy.deepcopy(self.list)
self.assertEquals(len(cpy), 2)
item = uniprot_kb.UniProtRecord()
cpy.extend([item])
self.assertEquals(len(cpy), 3)
self.assertEquals(cpy[2], item)
def setUp(self):
self.record = uniprot_kb.UniProtRecord(
3, 1, 35780, 333, "GAPDH", "P46406", "G3P_RABIT",
"Glyceraldehyde-3-phosphate dehydrogenase",
"Oryctolagus cuniculus", "UP000001811",
"MVKVGVNGFGRIGRLVTRAAFNSGKVDVVAINDPFIDLHYMVYMFQYDSTHGKFHGTVKAENGKLVINGKAITIFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHEKYDNSLKIVSNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGAAQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVVSCDFNSATHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMVHMASKE",
"9986")
def test_copy(self):
# test shallow copy (actually a deepcopy)
cpy = copy.copy(self.list)
self.assertEquals(self.list, cpy)
cpy[1].id = "P04797"
self.assertEquals(self.list, cpy)
cpy.append(uniprot_kb.UniProtRecord())
self.assertNotEquals(self.list, cpy)
# test deep copy
cpy = copy.deepcopy(self.list)
self.assertEquals(self.list, cpy)
cpy[1].id = "P02769"
self.assertNotEquals(self.list, cpy)
cpy.append(uniprot_kb.UniProtRecord())
self.assertNotEquals(self.list, cpy)
def test_len(self):
blank = uniprot_kb.UniProtRecordList()
self.assertEquals(len(blank), 0)
cpy = copy.copy(self.list)
self.assertEquals(len(cpy), 2)
cpy.append(uniprot_kb.UniProtRecord())
self.assertEquals(len(cpy), 3)
def setUp(self):
self.list = uniprot_kb.UniProtRecordList()
# GAPDH
self.list.append(
uniprot_kb.UniProtRecord(
3, 1, 35780, 333, "GAPDH", "P46406", "G3P_RABIT",
"Glyceraldehyde-3-phosphate dehydrogenase",
"Oryctolagus cuniculus", "UP000001811",
"MVKVGVNGFGRIGRLVTRAAFNSGKVDVVAINDPFIDLHYMVYMFQYDSTHGKFHGTVKAENGKLVINGKAITIFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHEKYDNSLKIVSNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGAAQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVVSCDFNSATHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMVHMASKE",
"9986"))
# BSA
self.list.append(
uniprot_kb.UniProtRecord(
4, 1, 69293, 607, "ALB", "P02769", "ALBU_BOVIN",
"Serum albumin", "Bos taurus", "UP000009136",
"MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVVSTQTALA",
"9913"))
def test_richcmp(self):
blank = uniprot_kb.UniProtRecord()
cpy = copy.copy(self.record)
self.assertNotEquals(self.record, blank)
self.assertEquals(self.record, cpy)
self.assertLess(blank, self.record)
self.assertLessEqual(blank, self.record)
self.assertLessEqual(cpy, self.record)
self.assertGreater(self.record, blank)
self.assertGreaterEqual(self.record, blank)
self.assertGreaterEqual(cpy, self.record)
def test_add(self):
cpy = copy.copy(self.list)
item = uniprot_kb.UniProtRecord()
# __add__
self.assertEquals(len(cpy + [item]), 3)
self.assertEquals(len(cpy), 2)
# __radd__
self.assertEquals(len([item] + cpy), 3)
self.assertEquals(len(cpy), 2)
# __iadd__
cpy += [item]
self.assertEquals(len(cpy), 3)
def test_count(self):
cpy = copy.copy(self.list)
self.assertEquals(cpy.count(self.list[0]), 1)
self.assertEquals(cpy.count(uniprot_kb.UniProtRecord()), 0)
def test_index(self):
cpy = copy.copy(self.list)
self.assertEquals(cpy.index(self.list[0]), 0)
with self.assertRaises(IndexError):
cpy.index(uniprot_kb.UniProtRecord())
def test_insert(self):
cpy = copy.deepcopy(self.list)
cpy.insert(0, uniprot_kb.UniProtRecord())
self.assertEquals(len(cpy), 3)
self.assertEquals(cpy[0], uniprot_kb.UniProtRecord())