def test_output_sans_desc():
read = FakeRecord()
read.name = 'foo'
read.sequence = 'ATCG'
fileobj = BytesIO()
write_fastx(read, fileobj)
assert fileobj.getvalue().decode('utf-8') == '>foo\nATCG\n'
def test_output_sans_desc():
read = FakeRecord()
read.name = 'foo'
read.sequence = 'ATCG'
fileobj = BytesIO()
write_fastx(read, fileobj)
assert fileobj.getvalue().decode('utf-8') == '>foo\nATCG\n'
def test_output_two_reads():
fileobj = BytesIO()
for i in range(2):
read = FakeRecord()
read.name = 'seq{}'.format(i)
read.sequence = 'GATTACA' * (i + 1)
write_fastx(read, fileobj)
testoutput = '>seq0\nGATTACA\n>seq1\nGATTACAGATTACA\n'
assert fileobj.getvalue().decode('utf-8') == testoutput
def test_output_two_reads():
fileobj = BytesIO()
for i in range(2):
read = FakeRecord()
read.name = 'seq{}'.format(i)
read.sequence = 'GATTACA' * (i + 1)
write_fastx(read, fileobj)
testoutput = '>seq0\nGATTACA\n>seq1\nGATTACAGATTACA\n'
assert fileobj.getvalue().decode('utf-8') == testoutput
def test_output_with_desc():
read = FakeRecord()
read.name = 'foo'
read.description = 'bar'
read.sequence = 'ATCG'
read.quality = '####'
fileobj = BytesIO()
write_fastx(read, fileobj)
assert fileobj.getvalue().decode('utf-8') == '@foo bar\nATCG\n+\n####\n'
def test_output_with_desc():
read = FakeRecord()
read.name = 'foo'
read.description = 'bar'
read.sequence = 'ATCG'
read.quality = '####'
fileobj = BytesIO()
write_fastx(read, fileobj)
assert fileobj.getvalue().decode('utf-8') == '@foo bar\nATCG\n+\n####\n'
def test_output_bad_mode():
read = FakeRecord()
read.name = 'foo'
read.description = 'bar'
read.sequence = 'ATCG'
read.quality = '####'
fileobj = StringIO()
with pytest.raises(AttributeError) as ae:
write_fastx(read, fileobj)
assert 'cannot call "write_fastx" on object' in str(ae)
def test_output_bad_mode():
read = FakeRecord()
read.name = 'foo'
read.description = 'bar'
read.sequence = 'ATCG'
read.quality = '####'
fileobj = StringIO()
with pytest.raises(AttributeError) as ae:
write_fastx(read, fileobj)
assert 'cannot call "write_fastx" on object' in str(ae)
