def __init__(self, opt_prefix="--rg-", *args, **kwargs):
ReadGroup.__init__(self, *args, **kwargs)
self._opt_prefix = opt_prefix
def test_rg_disallowed_key(self):
"""Test setting a read group object with a key not present in allowed keys"""
rg = ReadGroup("(?P<PU1>[0-9])_(?P<DATE>[0-9]+)_(?P<PU2>[A-Z0-9]+XX)_(?P<SM>P[0-9]+_[0-9]+)")
s = (rg.parse("../data/projects/J.Doe_00_01/P001_101/121015_BB002BBBXX/1_121015_BB002BBBXX_P001_101_1.fastq.gz"))
def test_os_sep(self, mock_re):
mock_re.return_value = None
rg = ReadGroup("(?P<SM>[a-zA-Z0-9]+)/(?P<PU>[A-Za-z0-9]+)/(?P<PU1>[0-9])_(?P<DT>[0-9]+)_(?P<PU2>[A-Z0-9]+XX)_(?P=SM)")
rg.parse("/data/projects/J.Doe_00_01/P001_101/121015_BB002BBBXX/1_121015_BB002BBBXX_P001_101_1.fastq.gz", "")
(args, kw) = mock_re.call_args
self.assertTrue(args[0].startswith('(?:[\\.\\w\\/]+)?\\/'))
def test_rg_parse_illumina_like(self):
"""Test parsing illumina-like-based file names"""
rg = ReadGroup("(?P<SM>[a-zA-Z0-9_]+)/(?P<DT>[0-9]+)_(?P<PU2>[A-Z0-9]+XX)/(?P<PU1>[0-9])_(?P=DT)_(?P=PU2)_(?P=SM)")
rg.parse("../data/projects/J.Doe_00_01/P001_101/121015_BB002BBBXX/1_121015_BB002BBBXX_P001_101_1.fastq.gz")
self.assertEqual("--date 2012-10-15 --identifier 1_121015_BB002BBBXX_P001_101 --platform-unit 1_BB002BBBXX --sample P001_101", str(rg))
