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(>?'))
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'))