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# Copyright 2016 by Stephen Marshall. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for cellosaurus module."""
import unittest
from Bio.ExPASy import cellosaurus
class TestCellosaurus(unittest.TestCase):
def test_read(self):
"""Test read function."""
with open("Cellosaurus/cell_lines_1.txt") as handle:
record = cellosaurus.read(handle)
self.assertEqual(record["ID"], "#15310-LN")
self.assertEqual(record["AC"], "CVCL_E548")
self.assertEqual(record["SY"], "15310-LN; TER461")
self.assertEqual(record["DR"][0], ("dbMHC", "48439"))
self.assertEqual(record["DR"][1], ("ECACC", "94050311"))
self.assertEqual(record["DR"][2], ("IHW", "IHW9326"))
self.assertEqual(record["DR"][3], ("IMGT/HLA", "10074"))
self.assertEqual(
record["WW"][0], "http://bioinformatics.hsanmartino.it/ecbr/cl326.html",
)
self.assertEqual(
record["CC"][0],
"Part of: 12th International Histocompatibility Workshop (12IHW) "
"cell line panel.",
)
self.assertEqual(record["CC"][1], "Transformant: EBV.")
self.assertEqual(record["OX"][0], "NCBI_TaxID=9606; ! Homo sapiens")
self.assertEqual(record["SX"], "Female")
self.assertEqual(record["CA"], "Transformed cell line")
def test_parse(self):
"""Test parsing function."""
with open("Cellosaurus/cell_lines_2.txt") as handle:
records = cellosaurus.parse(handle)
record = next(records)
self.assertEqual(record["ID"], "XP3OS")
self.assertEqual(record["AC"], "CVCL_3245")
self.assertEqual(record["AS"], "CVCL_F511")
self.assertEqual(record["SY"], "XP30S; GM04314")
self.assertEqual(record["DR"][0], ("CLO", "CLO_0019557"))
self.assertEqual(record["DR"][1], ("Coriell", "GM04314"))
self.assertEqual(record["DR"][2], ("JCRB", "JCRB0303"))
self.assertEqual(record["DR"][3], ("JCRB", "KURB1002"))
self.assertEqual(record["DR"][4], ("JCRB", "KURB1003"))
self.assertEqual(record["DR"][5], ("JCRB", "KURB1004"))
self.assertEqual(record["RX"][0], "PubMed=1372102;")
self.assertEqual(len(record["ST"]), 10)
self.assertEqual(record["ST"][0], "Source(s): JCRB")
self.assertEqual(record["ST"][1], "Amelogenin: X")
self.assertEqual(record["ST"][2], "CSF1PO: 10,11")
self.assertEqual(record["ST"][3], "D13S317: 9,11")
self.assertEqual(record["ST"][4], "D16S539: 9,12")
self.assertEqual(record["ST"][5], "D5S818: 10,11")
self.assertEqual(record["ST"][6], "D7S820: 11,12")
self.assertEqual(record["ST"][7], "TH01: 7")
self.assertEqual(record["ST"][8], "TPOX: 8,11")
self.assertEqual(record["ST"][9], "vWA: 14,16")
self.assertEqual(
record["DI"][0],
"NCIt; C3965; Xeroderma pigmentosum, complementation group A",
)
self.assertEqual(record["OX"][0], "NCBI_TaxID=9606; ! Homo sapiens")
self.assertEqual(record["SX"], "Female")
self.assertEqual(record["CA"], "Finite cell line")
record = next(records)
self.assertEqual(record["ID"], "1-5c-4")
self.assertEqual(record["AC"], "CVCL_2260")
self.assertEqual(
record["SY"],
"Clone 1-5c-4; Clone 1-5c-4 WKD of Chang Conjunctiva; "
"Wong-Kilbourne derivative of Chang conjunctiva; ChWK",
)
self.assertEqual(len(record["DR"]), 10)
self.assertEqual(record["DR"][0], ("CLO", "CLO_0002500"))
self.assertEqual(record["DR"][1], ("CLO", "CLO_0002501"))
self.assertEqual(record["DR"][2], ("CLDB", "cl793"))
self.assertEqual(record["DR"][3], ("CLDB", "cl794"))
self.assertEqual(record["DR"][4], ("CLDB", "cl795"))
self.assertEqual(record["DR"][5], ("ATCC", "CCL-20.2"))
self.assertEqual(record["DR"][6], ("BioSample", "SAMN03151673"))
self.assertEqual(record["DR"][7], ("ECACC", "88021103"))
self.assertEqual(record["DR"][8], ("IZSLER", "BS CL 93"))
self.assertEqual(record["DR"][9], ("KCLB", "10020.2"))
self.assertEqual(record["RX"][0], "PubMed=566722;")
self.assertEqual(record["RX"][1], "PubMed=19630270;")
self.assertEqual(record["RX"][2], "PubMed=20143388;")
self.assertEqual(
record["WW"][0],
"http://iclac.org/wp-content/uploads/Cross-Contaminations-v7_2.pdf",
)
self.assertEqual(
record["CC"][0],
"Problematic cell line: Contaminated. "
"Shown to be a HeLa derivative (PubMed 566722, PubMed 20143388).",
)
self.assertEqual(record["CC"][1], "Omics: Transcriptome analysis.")
self.assertEqual(record["ST"][0], "Source(s): ATCC; KCLB")
self.assertEqual(record["ST"][1], "Amelogenin: X")
self.assertEqual(record["ST"][2], "CSF1PO: 9,10")
self.assertEqual(record["ST"][3], "D13S317: 12,13.3")
self.assertEqual(record["ST"][4], "D16S539: 9,10")
self.assertEqual(record["ST"][5], "D3S1358: 15,18")
self.assertEqual(record["ST"][6], "D5S818: 11,12")
self.assertEqual(record["ST"][7], "D7S820: 8,12")
self.assertEqual(record["ST"][8], "FGA: 18,21")
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; C4029; Cervical adenocarcinoma")
self.assertEqual(record["OX"][0], "NCBI_TaxID=9606; ! Homo sapiens")
self.assertEqual(record["HI"][0], "CVCL_0030 ! HeLa")
self.assertEqual(record["SX"], "Female")
self.assertEqual(record["CA"], "Cancer cell line")
self.assertRaises(StopIteration, next, records)
def test__str__(self):
"""Test string function."""
with open("Cellosaurus/cell_lines_3.txt") as handle:
record = cellosaurus.read(handle)
text = (
"ID: ZZ-R 127 AC: CVCL_5418 AS: SY: ZZ-R DR: [('CCLV', 'CCLV-RIE 0127')] "
"RX: ['PubMed=19656987;', 'PubMed=19941903;'] WW: [] CC: [] ST: [] DI: [] "
"OX: ['NCBI_TaxID=9925; ! Capra hircus'] HI: [] OI: [] SX: CA: "
"Spontaneously immortalized cell line"
)
self.assertEqual(str(record), text)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=3)
unittest.main(testRunner=runner)
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