def test_fasta_file_object_not_a_file(self):
with pytest.raises(TypeError):
Reader('')
with pytest.raises(TypeError):
Reader([])
with pytest.raises(TypeError):
Reader(123)
def test_sequences_type_wrong_str(self, fasta_empty):
with pytest.raises(TypeError):
Reader(fasta_empty, sequences_type='')
with pytest.raises(TypeError):
Reader(fasta_empty, sequences_type=' ')
with pytest.raises(TypeError):
Reader(fasta_empty, sequences_type='wrong_type')
def test_single_fasta_file_rich(self, fasta_nucleotide_single,
fasta_nucleotide_single_contents,
fasta_aminoacid_single,
fasta_aminoacid_single_contents):
# nucleotide
fasta_nucleotide_reader = Reader(fasta_nucleotide_single,
sequences_type='nucleotide')
fastas_nucleotide = []
for fasta in fasta_nucleotide_reader:
fastas_nucleotide.append(fasta)
assert len(fastas_nucleotide) == 1
assert fastas_nucleotide[0].sequence_as_string(
) == fasta_nucleotide_single_contents[0][2]
assert fastas_nucleotide[0].id == fasta_nucleotide_single_contents[0][
0]
assert fastas_nucleotide[
0].description == fasta_nucleotide_single_contents[0][1]
assert fastas_nucleotide[0].sequence_type == 'nucleotide'
assert fastas_nucleotide[0].inferred_type is False
# aminoacid
fasta_aminoacid_reader = Reader(fasta_aminoacid_single,
sequences_type='aminoacid')
fastas_aminoacid = []
for fasta in fasta_aminoacid_reader:
fastas_aminoacid.append(fasta)
assert len(fastas_aminoacid) == 1
assert fastas_aminoacid[0].sequence_as_string(
) == fasta_aminoacid_single_contents[0][2]
assert fastas_aminoacid[0].id == fasta_aminoacid_single_contents[0][0]
assert fastas_aminoacid[
0].description == fasta_aminoacid_single_contents[0][1]
assert fastas_aminoacid[0].sequence_type == 'aminoacid'
assert fastas_aminoacid[0].inferred_type is False
def test_multiple_fasta_file_quick(self, fasta_nucleotide_multiple,
fasta_nucleotide_multiple_contents,
fasta_aminoacid_multiple,
fasta_aminoacid_multiple_contents):
# nucleotide
fasta_nucleotide_reader = Reader(fasta_nucleotide_multiple,
parse_method='quick')
fastas_nucleotide = []
for fasta in fasta_nucleotide_reader:
fastas_nucleotide.append(fasta)
assert fasta.sequence == fasta_nucleotide_multiple_contents[
len(fastas_nucleotide) - 1][2]
assert fasta.header == '>' + ' '.join(
(fasta_nucleotide_multiple_contents[len(fastas_nucleotide) -
1][0],
fasta_nucleotide_multiple_contents[len(fastas_nucleotide) -
1][1]))
assert len(fastas_nucleotide) == 17
# aminoacid
fasta_aminoacid_reader = Reader(fasta_aminoacid_multiple,
parse_method='quick')
fastas_aminoacid = []
for fasta in fasta_aminoacid_reader:
fastas_aminoacid.append(fasta)
assert fasta.sequence == fasta_aminoacid_multiple_contents[
len(fastas_aminoacid) - 1][2]
assert fasta.header == '>' + ' '.join(
(fasta_aminoacid_multiple_contents[len(fastas_aminoacid) -
1][0],
fasta_aminoacid_multiple_contents[len(fastas_aminoacid) -
1][1]))
assert len(fastas_aminoacid) == 20
def test_infer_type_not_bool(self, fasta_empty):
with pytest.raises(TypeError):
Reader(fasta_empty, infer_type='')
with pytest.raises(TypeError):
Reader(fasta_empty, infer_type=[])
with pytest.raises(TypeError):
Reader(fasta_empty, infer_type=123)
def test_parse_method_wrong_str(self, fasta_empty):
with pytest.raises(TypeError):
Reader(fasta_empty, parse_method='')
with pytest.raises(TypeError):
Reader(fasta_empty, parse_method=' ')
with pytest.raises(TypeError):
Reader(fasta_empty, parse_method='wrong_type')
def test_current_iterator(self, fasta_empty):
fasta_reader = Reader(fasta_empty)
assert fasta_reader._current_iterator is None
iterator = fasta_reader.__iter__()
assert fasta_reader._current_iterator == iterator
try: # test if is iterable
iter(fasta_reader._current_iterator)
except TypeError:
pytest.fail('Reader._current_iterator is not iterable.')
def test_sequences_type_aminoacid(self, fasta_aminoacid_multiple):
fasta_reader = Reader(fasta_aminoacid_multiple,
sequences_type='aminoacid')
assert fasta_reader.fasta_file is fasta_aminoacid_multiple
assert fasta_reader.sequences_type == 'aminoacid'
assert fasta_reader.infer_type is False
assert fasta_reader.parse_method == 'rich'
def test_sequences_type_nucleotide(self, fasta_nucleotide_multiple):
fasta_reader = Reader(fasta_nucleotide_multiple,
sequences_type='nucleotide')
assert fasta_reader.fasta_file is fasta_nucleotide_multiple
assert fasta_reader.sequences_type == 'nucleotide'
assert fasta_reader.infer_type is False
assert fasta_reader.parse_method == 'rich'
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_no_empty_lines(self, fasta_no_empty_lines,
fasta_no_empty_lines_contents):
fasta_reader = Reader(fasta_no_empty_lines, parse_method='quick')
fastas = []
for fasta in fasta_reader:
fastas.append(fasta)
assert fasta.sequence == fasta_no_empty_lines_contents[len(fastas)
- 1][2]
assert fasta.header == '>' + ' '.join(
(fasta_no_empty_lines_contents[len(fastas) - 1][0],
fasta_no_empty_lines_contents[len(fastas) - 1][1]))
assert len(fastas) == 2
def test_no_current_iterator(self, fasta_nucleotide_multiple,
fasta_nucleotide_multiple_contents):
fasta_reader = Reader(fasta_nucleotide_multiple,
sequences_type='nucleotide')
fasta = next(fasta_reader)
assert fasta.sequence_as_string(
) == fasta_nucleotide_multiple_contents[0][2]
assert fasta.id == fasta_nucleotide_multiple_contents[0][0]
assert fasta.description == fasta_nucleotide_multiple_contents[0][1]
assert fasta.sequence_type == 'nucleotide'
assert fasta.inferred_type is False
fasta = next(fasta_reader)
assert fasta.sequence_as_string(
) == fasta_nucleotide_multiple_contents[1][2]
assert fasta.id == fasta_nucleotide_multiple_contents[1][0]
assert fasta.description == fasta_nucleotide_multiple_contents[1][1]
assert fasta.sequence_type == 'nucleotide'
assert fasta.inferred_type is False
def test_fasta_file_object_closed(self, fasta_nucleotide_multiple):
fasta_nucleotide_multiple.close()
with pytest.raises(TypeError):
Reader(fasta_nucleotide_multiple)
def test_fasta_file_object_good(self, fasta_nucleotide_multiple):
fasta_reader = Reader(fasta_nucleotide_multiple)
assert fasta_reader.fasta_file is fasta_nucleotide_multiple
assert fasta_reader.sequences_type is None
assert fasta_reader.infer_type is False
assert fasta_reader.parse_method == 'rich'
def test__repr__(self, fasta_empty):
fasta_reader = Reader(fasta_empty)
assert repr(
fasta_reader) == 'fastaparser.Reader(%s)' % os.path.abspath(
fasta_empty.name)
def test_empty_fasta_file_quick(self, fasta_empty):
fasta_reader = Reader(fasta_empty, parse_method='quick')
fastas = []
for fasta in fasta_reader:
fastas.append(fasta)
assert len(fastas) == 0
def test_empty_fasta_file_rich(self, fasta_empty):
fasta_reader = Reader(fasta_empty)
fastas = []
for fasta in fasta_reader:
fastas.append(fasta)
assert len(fastas) == 0
def test_sequences_type_wrong_type(self, fasta_empty):
with pytest.raises(TypeError):
Reader(fasta_empty, sequences_type=[])
with pytest.raises(TypeError):
Reader(fasta_empty, sequences_type=123)
def test_closed_file(self, fasta_empty):
fasta_reader = Reader(fasta_empty)
fasta_empty.close()
with pytest.raises(TypeError):
fasta_reader.__iter__()
def test_current_iterator(self, fasta_empty):
fasta_reader = Reader(fasta_empty)
assert fasta_reader._current_iterator is None
def test_parse_method_wrong_type(self, fasta_empty):
with pytest.raises(TypeError):
Reader(fasta_empty, parse_method=[])
with pytest.raises(TypeError):
Reader(fasta_empty, parse_method=123)
def test_parse_method_quick(self, fasta_empty):
fasta_reader = Reader(fasta_empty, parse_method='quick')
assert fasta_reader.fasta_file is fasta_empty
assert fasta_reader.sequences_type is None
assert fasta_reader.infer_type is False
assert fasta_reader.parse_method == 'quick'
def test_infer_type_true(self, fasta_empty):
fasta_reader = Reader(fasta_empty, infer_type=True)
assert fasta_reader.fasta_file is fasta_empty
assert fasta_reader.sequences_type is None
assert fasta_reader.infer_type is True
assert fasta_reader.parse_method == 'rich'
