def test_fastareader():
with seqio.FastaReader("tests/data/simple.fasta") as f:
reads = list(f)
assert reads == simple_fasta
fasta = StringIO(">first_sequence\nSEQUENCE1\n>second_sequence\nSEQUENCE2\n")
reads = list(seqio.FastaReader(fasta))
assert reads == simple_fasta
def test_wrong_fasta_format():
fasta = StringIO(
dedent("""
# a comment
# another one
unexpected
>first_sequence
SEQUENCE1
>second_sequence
SEQUENCE2
"""))
reads = list(seqio.FastaReader(fasta))
def test_fastareader_with_comments():
fasta = StringIO(
dedent("""
# a comment
# another one
>first_sequence
SEQUENCE1
>second_sequence
SEQUENCE2
"""))
reads = list(seqio.FastaReader(fasta))
assert reads == simple_fasta
def test_context_manager():
filename = "tests/data/simple.fasta"
with open(filename) as f:
assert not f.closed
reads = list(seqio.open(f))
assert not f.closed
assert f.closed
with seqio.FastaReader(filename) as sr:
tmp_sr = sr
assert not sr.fp.closed
reads = list(sr)
assert not sr.fp.closed
assert tmp_sr.fp.closed
def test_fastareader_keeplinebreaks():
with seqio.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_fastareader():
with seqio.FastaReader("tests/data/simple.fasta") as f:
reads = list(f)
assert reads == simple_fasta