def test_autodetect_fastq_format(self):
path = os.path.join(self._tmpdir, 'tmp.fastq')
fmt = get_format(path)
with open_output(path, "w") as f:
for seq in simple_fastq:
f.write(fmt.format(seq))
assert list(openseq(path)) == simple_fastq
def test_autodetect_fastq_format(self):
path = os.path.join(self._tmpdir, 'tmp.fastq')
fmt = get_format(path)
with open_output(path, "w") as f:
for seq in simple_fastq:
f.write(fmt.format(seq))
assert list(openseq(path)) == simple_fastq
def test_write_qualities_to_fasta(self):
path = os.path.join(self._tmpdir, 'tmp.fasta')
fmt = get_format(path, qualities=True)
assert isinstance(fmt, FastaFormat)
with open_output(path, "w") as f:
for seq in simple_fastq:
f.write(fmt.format(seq))
assert list(openseq(path)) == simple_fasta
def test_write_qualities_to_fasta(self):
path = os.path.join(self._tmpdir, 'tmp.fasta')
fmt = get_format(path, qualities=True)
assert isinstance(fmt, FastaFormat)
with open_output(path, "w") as f:
for seq in simple_fastq:
f.write(fmt.format(seq))
assert list(openseq(path)) == simple_fasta
def test_fastq_qualities_missing(self):
with raises(ValueError):
path = os.path.join(self._tmpdir, 'tmp.fastq')
get_format(path, qualities=False)
def test_fastq_qualities_missing(self):
with raises(ValueError):
path = os.path.join(self._tmpdir, 'tmp.fastq')
get_format(path, qualities=False)