def __init__(self, options, filename):
genome = list(FASTA.from_file(filename))
assert len(genome) == 1, len(genome)
self._genome = genome[0].sequence.upper()
self._sequence = None
self._positions = None
self._annotations = None
self._mutate(options)
def __init__(self, options, filename):
genome = list(FASTA.from_file(filename))
assert len(genome) == 1, len(genome)
self._genome = genome[0].sequence.upper()
self._sequence = None
self._positions = None
self._annotations = None
self._mutate(options)
def test_fasta__from_file(func, tmp_path):
expected = [
FASTA("This_is_FASTA!", None, "ACGTN"),
FASTA("This_is_ALSO_FASTA!", None, "CGTNA"),
]
with func(tmp_path / "file", "wt") as handle:
for item in expected:
item.write(handle)
assert list(FASTA.from_file(tmp_path / "file")) == expected
def _setup(self, _config, temp):
self._update_ctl_file(source = self._control_file,
destination = os.path.join(temp, "template.ctl"))
os.symlink(os.path.abspath(self._trees_file), os.path.join(temp, "template.trees"))
with open(os.path.join(temp, "template.seqs"), "w") as handle:
for record in FASTA.from_file(self._sequence_file):
if record.name not in self._exclude_groups:
name = record.name
sequence = record.sequence.upper()
handle.write("%s\n" % (FASTA(name, None, sequence),))
def _setup(self, _config, temp):
self._update_ctl_file(source=self._control_file,
destination=os.path.join(temp, "template.ctl"))
os.symlink(os.path.abspath(self._trees_file),
os.path.join(temp, "template.trees"))
with open(os.path.join(temp, "template.seqs"), "w") as handle:
for record in FASTA.from_file(self._sequence_file):
if record.name not in self._exclude_groups:
name = record.name
sequence = record.sequence.upper()
handle.write("%s\n" % (FASTA(name, None, sequence), ))
def test_fasta__from_file__compressed_bz2():
expected = [FASTA("This_is_BZ_FASTA!", None, "CGTNA"),
FASTA("This_is_ALSO_BZ_FASTA!", None, "ACGTN")]
results = list(FASTA.from_file(test_file("fasta_file.fasta.bz2")))
assert_equal(results, expected)
def test_fasta__from_file__compressed_bz2():
expected = [FASTA("This_is_BZ_FASTA!", None, "CGTNA"),
FASTA("This_is_ALSO_BZ_FASTA!", None, "ACGTN")]
results = list(FASTA.from_file(test_file("fasta_file.fasta.bz2")))
assert_equal(results, expected)
