def process_cla_cid(fc):
print(' ~ [CLA -> CID]')
# Create a table to match cla to cid and associated cell line information
data = {}
with open(fc, 'r') as handle:
records = cellosaurus.parse(handle)
for i, record in enumerate(records):
data[record['AC']] = {
'ID': record['ID'],
'CA': record['CA'],
'SX': record['SX'],
'OX': [j.split(' ! ')[1] for j in record['OX']][0]
}
return (data)
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; ! H**o 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; ! H**o 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_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; ! H**o 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; ! H**o 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()