def test_context_manager(self):
filename = "tests/data/simple.fasta"
with open(filename, 'rb') as f:
assert not f.closed
_ = list(dnaio.open(f))
assert not f.closed
assert f.closed
with FastaReader(filename) as sr:
tmp_sr = sr
assert not sr._file.closed
_ = list(sr)
assert not sr._file.closed
assert tmp_sr._file is None
# Open it a second time
with FastaReader(filename):
pass
def test_with_comments(self):
fasta = BytesIO(
dedent("""
# a comment
# another one
>first_sequence
SEQUENCE1
>second_sequence
SEQUENCE2
""").encode())
reads = list(FastaReader(fasta))
assert reads == simple_fasta
def test_wrong_format(self):
fasta = BytesIO(
dedent("""# a comment
# another one
unexpected
>first_sequence
SEQUENCE1
>second_sequence
SEQUENCE2
""").encode())
with raises(FastaFormatError) as info:
list(FastaReader(fasta))
assert info.value.line == 2
def test_fastareader_keeplinebreaks(self):
with FastaReader("tests/data/simple.fasta", keep_linebreaks=True) as f:
reads = list(f)
assert reads[0] == simple_fasta[0]
assert reads[1].sequence == 'SEQUEN\nCE2'
def test_bytesio(self):
fasta = BytesIO(
b">first_sequence\nSEQUENCE1\n>second_sequence\nSEQUENCE2\n")
reads = list(FastaReader(fasta))
assert reads == simple_fasta
def test_file(self):
with FastaReader("tests/data/simple.fasta") as f:
reads = list(f)
assert reads == simple_fasta