# 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)