# 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. import os import unittest from Bio.ExPASy import cellosaurus class TestCellosaurus(unittest.TestCase): def test_read(self): """Test read function""" handle = open("Cellosaurus/cell_lines_1.txt") record = cellosaurus.read(handle) self.assertEquals(record["ID"], '#15310-LN') self.assertEqual(record["AC"], 'CVCL_E548') self.assertEqual(record["SY"], '15310-LN; TER461') self.assertEqual(record["DR"][0], tuple(('dbMHC', '48439'))) self.assertEqual(record["DR"][1], tuple(('ECACC', '94050311'))) self.assertEqual(record["DR"][2], tuple(('IHW', 'IHW9326'))) self.assertEqual(record["DR"][3], tuple(('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') handle.close() def test_parse(self): """Test parsing function""" handle = open("Cellosaurus/cell_lines_2.txt") 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], tuple(('CLO', 'CLO_0019557'))) self.assertEqual(record["DR"][1], tuple(('Coriell', 'GM04314'))) self.assertEqual(record["DR"][2], tuple(('JCRB', 'JCRB0303'))) self.assertEqual(record["DR"][3], tuple(('JCRB', 'KURB1002'))) self.assertEqual(record["DR"][4], tuple(('JCRB', 'KURB1003'))) self.assertEqual(record["DR"][5], tuple(('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], tuple(('CLO', 'CLO_0002500'))) self.assertEqual(record["DR"][1], tuple(('CLO', 'CLO_0002501'))) self.assertEqual(record["DR"][2], tuple(('CLDB', 'cl793'))) self.assertEqual(record["DR"][3], tuple(('CLDB', 'cl794'))) self.assertEqual(record["DR"][4], tuple(('CLDB', 'cl795'))) self.assertEqual(record["DR"][5], tuple(('ATCC', 'CCL-20.2'))) self.assertEqual(record["DR"][6], tuple(('BioSample', 'SAMN03151673'))) self.assertEqual(record["DR"][7], tuple(('ECACC', '88021103'))) self.assertEqual(record["DR"][8], tuple(('IZSLER', 'BS CL 93'))) self.assertEqual(record["DR"][9], tuple(('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) handle.close() def test__str__(self): """Test string function""" handle = open("Cellosaurus/cell_lines_3.txt") record = cellosaurus.read(handle) input = "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.assertEquals(record.__str__(), input) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=3) unittest.main(testRunner=runner)