def test_invalid(self):
dirname = 'bad'
dirpath = self.get_data_path(dirname)
transformer = self.get_transformer(EMPSingleEndDirFmt,
BarcodeSequenceFastqIterator)
with self.assertRaises(ValidationError):
transformer(EMPSingleEndDirFmt(dirpath, mode='r'))
transformer = self.get_transformer(EMPSingleEndCasavaDirFmt,
EMPSingleEndDirFmt)
with self.assertRaises(ValidationError):
transformer(EMPSingleEndCasavaDirFmt(dirpath, 'r'))
def test_emp_se_multiplexed_format_barcode_sequence_iterator(self):
transformer1 = self.get_transformer(EMPSingleEndCasavaDirFmt,
EMPSingleEndDirFmt)
transformer2 = self.get_transformer(EMPSingleEndDirFmt,
BarcodeSequenceFastqIterator)
dirname = 'emp_multiplexed_single_end'
dirpath = self.get_data_path(dirname)
emp_demultiplexed = \
transformer1(EMPSingleEndCasavaDirFmt(dirpath, mode='r'))
bsi = transformer2(EMPSingleEndDirFmt(emp_demultiplexed, mode='r'))
bsi = list(bsi)
self.assertEqual(len(bsi), 250)
self.assertEqual(bsi[0][0],
('@M00176:17:000000000-A0CNA:1:1:15487:1773 1:N:0:0',
'TTAGGCATCTCG', '+', 'B@@FFFFFHHHH'))
self.assertEqual(
bsi[0][1],
('@M00176:17:000000000-A0CNA:1:1:15487:1773 1:N:0:0',
'GCTTAGGGATTTTATTGTTATCAGGGTTAATCGTGCCAAGAAAAGCGGCATGGTCAATATAAC'
'CAGTAGTGTTAACAGTCGGGAGAGGAGTGGCATTAACACCATCCTTCATGAACTTAATCCACT'
'GTTCACCATAAACGTGACGATGAGG', '+',
'C@CFFFFFHHFHHGIJJ?FFHEIIIIHGEIIFHGIIJHGIGBGB?DHIIJJJJCFCHIEGIGG'
'HGFAEDCEDBCCEEA.;>?BB=288A?AB709@:3:A:C88CCD@CC444@>>34>>ACC:?C'
'CD<CDCA>A@A>:<?B@?<((2(>?'))