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ran black on test_cellosaurus.py

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This commit is contained in:
Judith Bernett
2024-02-02 14:38:08 +01:00
committed by Peter Cock
parent 8d2191aee1
commit 4ff9ed8b10
1 changed files with 32 additions and 18 deletions
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50
Tests/test_cellosaurus.py
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@ -17,7 +17,10 @@ class TestCellosaurus(unittest.TestCase):
record = cellosaurus.read(handle)
self.assertEqual(record["ID"], "#15310-LN")
self.assertEqual(record["AC"], "CVCL_E548")
self.assertEqual(record["SY"], "15310-LN; TER461; TER-461; Ter 461; TER479; TER-479; Ter 479; Extract 519")
self.assertEqual(
record["SY"],
"15310-LN; TER461; TER-461; Ter 461; TER479; TER-479; Ter 479; Extract 519",
)
self.assertEqual(record["DR"][0], ("dbMHC", "48439"))
self.assertEqual(record["DR"][1], ("ECACC", "94050311"))
self.assertEqual(record["DR"][2], ("IHW", "IHW09326"))
@ -34,29 +37,28 @@ class TestCellosaurus(unittest.TestCase):
"Part of: 12th International Histocompatibility Workshop (12IHW) "
"cell line panel.",
)
self.assertEqual(
record["CC"][1],
"Population: Caucasian; French Canadian."
)
self.assertEqual(record["CC"][1], "Population: Caucasian; French Canadian.")
self.assertEqual(
record["CC"][2],
"HLA typing: A*03,25; B*37:01:01:01,47:01:01:03; C*06; DPA1*01; DPB1*04:01:01; DQA1*01:01:01:01,"
"01:03:01; DQB1*05:01:01;06:03:01:02; DRB1*01:01:01,14:17; DRB3*01:01 (IPD-IMGT/HLA=10074)."
"01:03:01; DQB1*05:01:01;06:03:01:02; DRB1*01:01:01,14:17; DRB3*01:01 (IPD-IMGT/HLA=10074).",
)
self.assertEqual(
record["CC"][3],
"Transformant: NCBI_TaxID; 10376; Epstein-Barr virus (EBV).",
)
self.assertEqual(record["CC"][3], "Transformant: NCBI_TaxID; 10376; Epstein-Barr virus (EBV).")
self.assertEqual(
record["CC"][4],
"Derived from site: In situ; Peripheral blood; UBERON=UBERON_0000178."
)
self.assertEqual(
record["CC"][5],
"Cell type: B-cell; CL=CL_0000236."
"Derived from site: In situ; Peripheral blood; UBERON=UBERON_0000178.",
)
self.assertEqual(record["CC"][5], "Cell type: B-cell; CL=CL_0000236.")
self.assertEqual(record["OX"][0], "NCBI_TaxID=9606; ! Homo sapiens (Human)")
self.assertEqual(record["SX"], "Female")
self.assertEqual(record["AG"], "Age unspecified")
self.assertEqual(record["CA"], "Transformed cell line")
self.assertEqual(record["DT"], "Created: 22-10-12; Last updated: 30-01-24; Version: 18")
self.assertEqual(
record["DT"], "Created: 22-10-12; Last updated: 30-01-24; Version: 18"
)
def test_parse(self):
"""Test parsing function."""
@ -66,7 +68,9 @@ class TestCellosaurus(unittest.TestCase):
self.assertEqual(record["ID"], "XP3OS")
self.assertEqual(record["AC"], "CVCL_3245")
self.assertEqual(record["AS"], "CVCL_F511")
self.assertEqual(record["SY"], "Xeroderma Pigmentosum 3 OSaka; GM04314; GM04314B; GM4314")
self.assertEqual(
record["SY"], "Xeroderma Pigmentosum 3 OSaka; GM04314; GM04314B; GM4314"
)
self.assertEqual(record["DR"][0], ("CLO", "CLO_0019557"))
self.assertEqual(record["DR"][1], ("Coriell", "GM04314"))
self.assertEqual(record["DR"][2], ("GEO", "GSM1338611"))
@ -115,7 +119,9 @@ class TestCellosaurus(unittest.TestCase):
self.assertEqual(record["SX"], "Female")
self.assertEqual(record["AG"], "5Y")
self.assertEqual(record["CA"], "Finite cell line")
self.assertEqual(record["DT"], "Created: 04-04-12; Last updated: 29-06-23; Version: 20")
self.assertEqual(
record["DT"], "Created: 04-04-12; Last updated: 29-06-23; Version: 20"
)
record = next(records)
self.assertEqual(record["ID"], "1-5c-4")
@ -151,7 +157,10 @@ class TestCellosaurus(unittest.TestCase):
"Problematic cell line: Contaminated. Shown to be a HeLa derivative (PubMed=566722; PubMed=20143388). "
"Originally thought to originate from the conjunctiva of a child.",
)
self.assertEqual(record["CC"][1], "Registration: International Cell Line Authentication Committee, Register of Misidentified Cell Lines; ICLAC-00298.")
self.assertEqual(
record["CC"][1],
"Registration: International Cell Line Authentication Committee, Register of Misidentified Cell Lines; ICLAC-00298.",
)
self.assertEqual(record["ST"][0], "Source(s): ATCC; KCLB")
self.assertEqual(record["ST"][1], "Amelogenin: X")
self.assertEqual(record["ST"][2], "CSF1PO: 9,10")
@ -164,13 +173,18 @@ class TestCellosaurus(unittest.TestCase):
self.assertEqual(record["ST"][9], "TH01: 7")
self.assertEqual(record["ST"][10], "TPOX: 8,12")
self.assertEqual(record["ST"][11], "vWA: 16,18")
self.assertEqual(record["DI"][0], "NCIt; C27677; Human papillomavirus-related cervical adenocarcinoma")
self.assertEqual(
record["DI"][0],
"NCIt; C27677; Human papillomavirus-related cervical adenocarcinoma",
)
self.assertEqual(record["OX"][0], "NCBI_TaxID=9606; ! Homo sapiens (Human)")
self.assertEqual(record["HI"][0], "CVCL_0030 ! HeLa")
self.assertEqual(record["SX"], "Female")
self.assertEqual(record["AG"], "30Y6M")
self.assertEqual(record["CA"], "Cancer cell line")
self.assertEqual(record["DT"], "Created: 04-04-12; Last updated: 05-10-23; Version: 25")
self.assertEqual(
record["DT"], "Created: 04-04-12; Last updated: 05-10-23; Version: 25"
)
self.assertRaises(StopIteration, next, records)
def test__str__(self):