def test_write_sequence_object(self):
with FastaWriter(self.path) as fw:
fw.write(SequenceRecord("name", "CCATA"))
fw.write(SequenceRecord("name2", "HELLO"))
assert fw._file.closed
with open(self.path) as t:
assert t.read() == '>name\nCCATA\n>name2\nHELLO\n'
def test(self):
with FastaWriter(self.path) as fw:
fw.write("name", "CCATA")
fw.write("name2", "HELLO")
assert fw._file.closed
with open(self.path) as t:
assert t.read() == '>name\nCCATA\n>name2\nHELLO\n'
def test_write_to_file_like_object(self):
bio = BytesIO()
with FastaWriter(bio) as fw:
fw.write(SequenceRecord("name", "CCATA"))
fw.write(SequenceRecord("name2", "HELLO"))
assert bio.getvalue() == b'>name\nCCATA\n>name2\nHELLO\n'
assert not bio.closed
assert not fw._file.closed
def test_linelength(self):
with FastaWriter(self.path, line_length=3) as fw:
fw.write("r1", "ACG")
fw.write("r2", "CCAT")
fw.write("r3", "TACCAG")
assert fw._file.closed
with open(self.path) as t:
d = t.read()
assert d == '>r1\nACG\n>r2\nCCA\nT\n>r3\nTAC\nCAG\n'
def test_fasta_writer_repr(tmp_path):
with FastaWriter(tmp_path / "out.fasta") as fw:
repr(fw)
def test_write_zero_length_sequence_record(self):
bio = BytesIO()
with FastaWriter(bio) as fw:
fw.write(SequenceRecord("name", ""))
assert bio.getvalue() == b'>name\n\n', '{!r}'.format(bio.getvalue())
