def test(self):
with 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(FastaReader(fasta))
assert reads == simple_fasta
def parse(self, spec, cmdline_type='back'):
"""Parse an adapter specification not using ``file:`` notation and return
an object of an appropriate Adapter class. The notation for anchored
5' and 3' adapters is supported. If the name parameter is None, then
an attempt is made to extract the name from the specification
(If spec is 'name=ADAPTER', name will be 'name'.)
Args:
spec: The adapter spec.
name: The adapter name. If not provided, one is automatically
generated.
cmdline_type: describes which commandline parameter was used (``-a``
is 'back', ``-b`` is 'anywhere', and ``-g`` is 'front').
TODO: describe the adapter spec format
Returns:
An :class:`Adapter` instance.
"""
if spec.startswith('file:'):
# read adapter sequences from a file
with FastaReader(spec[5:]) as fasta:
for record in fasta:
name = record.name.split(None, 1)[0]
yield self.parse_from_spec(record.sequence, cmdline_type,
name)
else:
yield self.parse_from_spec(spec, cmdline_type)
def test_context_manager(self):
filename = "tests/data/simple.fasta"
with open(filename) as f:
assert not f.closed
reads = list(openseq(f))
assert not f.closed
assert f.closed
with FastaReader(filename) as sr:
tmp_sr = sr
assert not sr._file.closed
reads = list(sr)
assert not sr._file.closed
assert tmp_sr._file is None
# Open it a second time
with FastaReader(filename) as sr:
pass
def test_with_comments(self):
fasta = StringIO(
dedent("""
# a comment
# another one
>first_sequence
SEQUENCE1
>second_sequence
SEQUENCE2
"""))
reads = list(FastaReader(fasta))
assert reads == simple_fasta
def test_wrong_format(self):
with raises(FormatError):
fasta = StringIO(
dedent("""
# a comment
# another one
unexpected
>first_sequence
SEQUENCE1
>second_sequence
SEQUENCE2
"""))
reads = list(FastaReader(fasta))
def load_from_fasta(self, fasta):
"""Load adapter data from a FASTA file.
Args:
fasta: FASTA file.
"""
close = False
if isinstance(fasta, str):
fasta = open(fasta, 'rt')
close = True
num_records = None
with FastaReader(fasta) as fasta:
for num_records, record in enumerate(fasta, 1):
name = record.name.split(None, 1)[0]
seq = record.sequence
self.add(name, seq)
if close:
fasta.close()
return num_records
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'