def test_fasta_file_object_not_a_file(self):
with pytest.raises(TypeError):
Writer('')
with pytest.raises(TypeError):
Writer([])
with pytest.raises(TypeError):
Writer(123)
def test_fasta_sequence_wrong_type(self, fasta_temporary_file):
with pytest.raises(TypeError):
fasta_writer = Writer(fasta_temporary_file)
fasta_writer.writefastas(123)
with pytest.raises(TypeError):
fasta_writer = Writer(fasta_temporary_file)
fasta_writer.writefastas(None)
with pytest.raises(TypeError):
fasta_writer = Writer(fasta_temporary_file)
fasta_writer.writefastas([1, 2])
def test_fasta_sequence_wrong_type(self, fasta_temporary_file):
with pytest.raises(TypeError):
fasta_writer = Writer(fasta_temporary_file)
fasta_writer.writefasta('')
with pytest.raises(TypeError):
fasta_writer = Writer(fasta_temporary_file)
fasta_writer.writefasta(123)
with pytest.raises(TypeError):
fasta_writer = Writer(fasta_temporary_file)
fasta_writer.writefasta([])
with pytest.raises(TypeError):
fasta_writer = Writer(fasta_temporary_file)
fasta_writer.writefasta((1, 2))
def test_fasta_sequence_fastasequence_objects(self,
fasta_nucleotide_multiple,
fasta_temporary_file):
fasta_reader = Reader(fasta_nucleotide_multiple)
fasta_writer = Writer(fasta_temporary_file)
fasta_writer.writefastas(fasta_reader)
# at this point the 2 files should be equal
compare_2_files(fasta_nucleotide_multiple, fasta_temporary_file)
def test_fasta_sequence_tuple(self, fasta_nucleotide_single,
fasta_temporary_file):
fasta_reader = Reader(fasta_nucleotide_single)
fasta_writer = Writer(fasta_temporary_file)
fasta = next(fasta_reader)
fasta_writer.writefasta(
(fasta.formatted_definition_line(), fasta.formatted_sequence()))
# at this point the 2 files should be equal
compare_2_files(fasta_nucleotide_single, fasta_temporary_file)
def test_fasta_sequence_fastasequence_object(self, fasta_nucleotide_single,
fasta_temporary_file):
fasta_reader = Reader(fasta_nucleotide_single)
fasta_writer = Writer(fasta_temporary_file)
fasta_writer.writefasta(
next(fasta_reader
)) # only a single FASTA sequence in fasta_nucleotide_single
# at this point the 2 files should be equal
compare_2_files(fasta_nucleotide_single, fasta_temporary_file)
def test_fasta_sequence_tuples(self, fasta_nucleotide_multiple,
fasta_temporary_file):
fasta_reader = Reader(fasta_nucleotide_multiple)
fasta_writer = Writer(fasta_temporary_file)
fastas = [(fasta.formatted_definition_line(),
fasta.formatted_sequence()) for fasta in fasta_reader]
fasta_writer.writefastas(fastas)
# at this point the 2 files should be equal
compare_2_files(fasta_nucleotide_multiple, fasta_temporary_file)
def test_fasta_file_object_closed(self, fasta_temporary_file):
fasta_temporary_file.close()
with pytest.raises(TypeError):
Writer(fasta_temporary_file)
def test_fasta_file_object_good(self, fasta_temporary_file):
fasta_writer = Writer(fasta_temporary_file)
assert fasta_writer.fasta_file is fasta_temporary_file
def test__repr__(self, fasta_temporary_file):
fasta_writer = Writer(fasta_temporary_file)
assert repr(
fasta_writer) == 'fastaparser.Writer(%s)' % os.path.abspath(
fasta_temporary_file.name)