# 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; 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")) self.assertEqual(record["DR"][3], ("IPD-IMGT/HLA", "10074")) self.assertEqual(record["DR"][4], ("Wikidata", "Q54398957")) self.assertEqual( record["WW"][0], "http://pathology.ucla.edu/workfiles/360cx.pdf" ) self.assertEqual( record["WW"][1], "http://pathology.ucla.edu/workfiles/370cx.pdf" ) self.assertEqual( record["CC"][0], "Part of: 12th International Histocompatibility Workshop (12IHW) " "cell line panel.", ) 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).", ) 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.") 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" ) 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"], "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")) self.assertEqual(record["DR"][3], ("JCRB", "JCRB0303")) self.assertEqual(record["DR"][4], ("JCRB", "KURB1002")) self.assertEqual(record["DR"][5], ("JCRB", "KURB1003")) self.assertEqual(record["DR"][6], ("JCRB", "KURB1004")) self.assertEqual(record["DR"][7], ("Wikidata", "Q54994928")) self.assertEqual(record["RX"][0], "CelloPub=CLPUB00447;") self.assertEqual(record["RX"][1], "PubMed=832273;") self.assertEqual(record["RX"][2], "PubMed=1372102;") self.assertEqual(record["RX"][3], "PubMed=1702221;") self.assertEqual(record["RX"][4], "PubMed=2570806;") self.assertEqual(record["RX"][5], "PubMed=7000335;") self.assertEqual(record["RX"][6], "PubMed=7830260;") self.assertEqual(record["RX"][7], "PubMed=9671271;") self.assertEqual(record["RX"][8], "PubMed=27197874;") self.assertEqual(len(record["CC"]), 6) self.assertEqual(len(record["ST"]), 17) self.assertEqual(record["ST"][0], "Source(s): JCRB; PubMed=27197874") 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], "D18S51: 13") self.assertEqual(record["ST"][6], "D21S11: 29,30") self.assertEqual(record["ST"][7], "D3S1358: 15,16") self.assertEqual(record["ST"][8], "D5S818: 10,11") self.assertEqual(record["ST"][9], "D7S820: 11,12") self.assertEqual(record["ST"][10], "D8S1179: 13,15") self.assertEqual(record["ST"][11], "FGA: 22,23") self.assertEqual(record["ST"][12], "Penta D: 9") self.assertEqual(record["ST"][13], "Penta E: 14,17") self.assertEqual(record["ST"][14], "TH01: 7") self.assertEqual(record["ST"][15], "TPOX: 8,11") self.assertEqual(record["ST"][16], "vWA: 14,16") self.assertEqual( record["DI"][0], "NCIt; C3965; Xeroderma pigmentosum, complementation group A", ) self.assertEqual( record["DI"][1], "ORDO; Orphanet_910; Xeroderma pigmentosum", ) self.assertEqual(record["OX"][0], "NCBI_TaxID=9606; ! Homo sapiens (Human)") 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" ) 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"]), 11) 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["DR"][10], ("Wikidata", "Q54399838")) self.assertEqual(record["RX"][0], "DOI=10.1007/BF02618370;") self.assertEqual(record["RX"][1], "PubMed=566722;") self.assertEqual(record["RX"][2], "PubMed=19630270;") self.assertEqual(record["RX"][3], "PubMed=20143388;") self.assertEqual( record["WW"][0], "https://iclac.org/wp-content/uploads/Cross-Contaminations_v12_distribution.xlsx", ) self.assertEqual(len(record["CC"]), 6) self.assertEqual( record["CC"][0], "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["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; 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.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'), ('Wikidata', 'Q54996143')] RX: " "['PubMed=19656987;', 'PubMed=19941903;', 'PubMed=26082457;', 'PubMed=27795464;', 'PubMed=32851014;', " "'PubMed=34737324;'] WW: [] CC: ['Virology: Susceptible to infection by foot-and-mouth disease virus.', " "'Derived from site: In situ; Fetal oral cavity, tongue; UBERON=UBERON_0010056.'] ST: [] DI: [] OX: [" "'NCBI_TaxID=9925; ! Capra hircus (Goat)'] HI: [] OI: [] SX: Sex unspecified AG: Fetus CA: Spontaneously " "immortalized cell line DT: Created: 04-04-12; Last updated: 29-06-23; Version: 15" ) self.assertEqual(str(record), text) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=3) unittest.main(testRunner=runner)