def test_fastqreader_dos(self):
# DOS line breaks
with open('tests/data/dos.fastq', 'rb') as f:
assert b'\r\n' in f.read()
with FastqReader("tests/data/dos.fastq") as f:
dos_reads = list(f)
with FastqReader("tests/data/small.fastq") as f:
unix_reads = list(f)
assert dos_reads == unix_reads
def test_two_header_detection(self):
fastq = BytesIO(b'@r1\nACG\n+r1\nHHH\n@r2\nT\n+r2\n#\n')
with FastqReader(fastq) as fq:
assert fq.two_headers
list(fq)
fastq = BytesIO(b'@r1\nACG\n+\nHHH\n@r2\nT\n+r2\n#\n')
with FastqReader(fastq) as fq:
assert not fq.two_headers
list(fq)
def test_half_record_line_numbers(self):
fastq = BytesIO(b'@r\nACG\n+\nHH\n')
# Choose the buffer size such that only parts of the record fit
# We want to ensure that the line number is reset properly
# after the record has been half-parsed
buffer_size = len('@r\nACG\n+\n')
with raises(FastqFormatError) as info:
with FastqReader(fastq, buffer_size=buffer_size) as fq:
list(fq) # pragma: no cover
assert 'Length of sequence and qualities differ' in info.value.message
assert info.value.line == 3
def test_context_manager(self):
filename = "tests/data/simple.fastq"
with open(filename, 'rb') as f:
assert not f.closed
_ = list(dnaio.open(f))
assert not f.closed
assert f.closed
with FastqReader(filename) as sr:
tmp_sr = sr
assert not sr._file.closed
_ = list(sr)
assert not sr._file.closed
assert tmp_sr._file is None
def test_second_header_not_equal(self):
fastq = BytesIO(b'@r1\nACG\n+xy\nXXX\n')
with raises(FastqFormatError) as info:
with FastqReader(fastq) as fq:
list(fq) # pragma: no cover
assert "Sequence descriptions don't match" in info.value.message
def test_differing_lengths(self, s, line):
fastq = BytesIO(s)
with raises(FastqFormatError) as info:
with FastqReader(fastq) as fq:
list(fq)
assert info.value.line == line
def test_fastq_incomplete(self, s, line):
fastq = BytesIO(s)
with raises(FastqFormatError) as info:
with FastqReader(fastq) as fq:
list(fq)
assert info.value.line == line
def test_empty_fastq(self):
with FastqReader(BytesIO(b'')) as fq:
assert list(fq) == []
def test_fastq_wrongformat(self):
with raises(FastqFormatError) as info:
with FastqReader("tests/data/withplus.fastq") as f:
list(f) # pragma: no cover
assert info.value.line == 2
def test_fastqreader_buffersize_too_small(self):
with raises(ValueError) as e:
with FastqReader("tests/data/simple.fastq", buffer_size=0) as f:
_ = list(f) # pragma: no cover
assert "buffer size too small" in e.value.args[0]
def test_fastqreader_buffersize(self, buffer_size):
with FastqReader("tests/data/simple.fastq",
buffer_size=buffer_size) as f:
reads = list(f)
assert reads == simple_fastq
def test_fastqreader(self):
with FastqReader(SIMPLE_FASTQ) as f:
reads = list(f)
assert reads == simple_fastq
def test_fastqreader(self):
with FastqReader("tests/data/simple.fastq") as f:
reads = list(f)
assert reads == simple_fastq