def setUp(self):
self.records = [
fastq_pb2.FastqRecord(id='id1', sequence='ACGTG', quality='ABCDE'),
fastq_pb2.FastqRecord(id='id2', sequence='ATTT', quality='ABC@'),
fastq_pb2.FastqRecord(id='ID3',
description='multi desc',
sequence='GATAC',
quality='ABC@!'),
]
def setUp(self):
writer_options = fastq_pb2.FastqWriterOptions()
out_fname = test_utils.test_tmpfile('output.fastq')
self.writer = fastq_writer.FastqWriter.to_file(out_fname,
writer_options)
self.expected_fastq_content = [
'@NODESC:header\n',
'GATTACA\n',
'+\n',
'BB>B@FA\n',
'@M01321:49:000000000-A6HWP:1:1101:17009:2216 1:N:0:1\n',
'CGTTAGCGCAGGGGGCATCTTCACACTGGTGACAGGTAACCGCCGTAGTAAAGGTTCCGCCTTTCACT\n',
'+\n',
'AAAAABF@BBBDGGGG?FFGFGHBFBFBFABBBHGGGFHHCEFGGGGG?FGFFHEDG3EFGGGHEGHG\n',
'@FASTQ contains multiple spaces in description\n',
'CGGCTGGTCAGGCTGACATCGCCGCCGGCCTGCAGCGAGCCGCTGC\n',
'+\n',
'FAFAF;F/9;.:/;999B/9A.DFFF;-->.AAB/FC;9-@-=;=.\n',
'@FASTQ_with_trailing_space\n',
'CGG\n',
'+\n',
'FAD\n',
]
self.record = fastq_pb2.FastqRecord(id='ID',
description='desc',
sequence='ACGTAC',
quality='ABCDEF')
def _raw_next(self):
record = fastq_pb2.FastqRecord()
not_done = self._cc_iterable.PythonNext(record)
return record, not_done