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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.
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)
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