def test_get_code(self):
"""correctly return the genetic code"""
for code_id in [1, "1", "Standard Nuclear", DEFAULT]:
got = get_code(code_id)
self.assertEqual(got, DEFAULT)
got = get_code(2)
self.assertEqual(got.name.lower(), "vertebrate mitochondrial")
def translate_frames(seq, moltype=None, gc=1, allow_rc=False):
"""translates a nucleic acid sequence
Parameters
----------
moltype
molecular type, must be either DNA or RNA
gc
identifer for a genetic code or a genetic code instance
allow_rc : bool
includes frames sequence reverse complement
Returns
-------
[(frame, translation), ..]
Reverse complement frame numbers are negative
"""
gc = get_code(gc)
if moltype:
moltype = get_moltype(moltype)
seq = moltype.make_seq(seq)
translations = gc.sixframes(seq)
if not allow_rc:
translations = translations[:3]
return translations
def __init__(self,
moltype="dna",
gc=1,
allow_rc=False,
trim_terminal_stop=True):
"""generates aa sequences
Parameters
----------
moltype : str
molecular type, must be either DNA or RNA
gc
identifier for a genetic code or a genetic code instance
trim_terminal_stop : bool
exclude terminal stop codon from seqs
Returns
-------
A sequence collection. Sequences that could not be translated
are excluded.
"""
super(translate_seqs, self).__init__(
input_types=self._input_types,
output_types=self._output_types,
data_types=self._data_types,
)
self._formatted_params()
moltype = get_moltype(moltype)
assert moltype.label.lower() in ("dna", "rna"), "Invalid moltype"
self._moltype = moltype
self._gc = get_code(gc)
self._trim_terminal_stop = trim_terminal_stop
self.func = self.get_translated
def test_repr_html(self):
"""exercising the _repr_html_ method"""
gc = get_code(1)
got = gc._repr_html_().strip()
self.assertTrue(got.startswith("<table>"))
self.assertTrue(got.endswith("</table>"))
self.assertIn("Standard Nuclear", got)
def __init__(
self,
*positions,
fourfold_degenerate=False,
gc="Standard Nuclear",
moltype="dna",
):
"""selects the indicated codon positions from an alignment
Parameters
----------
positions
either an integer (1, 2, 3), or a tuple of position numbers,
e.g. 3 is third position, (1,2) is first and second codon position
fourfold_degenerate : bool
if True, returns third positions from four-fold degenerate codons.
Overrides positions.
gc
identifer for a genetic code or a genetic code instance
moltype : str
molecular type, must be either DNA or RNA
"""
super(take_codon_positions, self).__init__(
input_types=self._input_types,
output_types=self._output_types,
data_types=self._data_types,
)
self._formatted_params()
assert moltype is not None
moltype = get_moltype(moltype)
assert moltype.label.lower() in ("dna", "rna"), "Invalid moltype"
self._moltype = moltype
self._four_fold_degen = fourfold_degenerate
self._fourfold_degen_sets = None
if fourfold_degenerate:
gc = get_code(gc)
sets = get_fourfold_degenerate_sets(
gc, alphabet=moltype.alphabet, as_indices=True
)
self._fourfold_degen_sets = sets
self.func = self.take_fourfold_positions
return
assert (
1 <= min(positions) <= 3 and 1 <= max(positions) <= 3
), "Invalid codon positions"
by_index = True if len(positions) == 1 else False
if by_index:
positions = positions[0] - 1
self.func = self.take_codon_position
else:
positions = tuple(p - 1 for p in sorted(positions))
self.func = self.take_codon_positions
self._positions = positions
def test_repr_html(self):
"""exercising the _repr_html_ method"""
gc = get_code(1)
got = gc._repr_html_().strip()
self.assertTrue('<div class="c3table">' in got
or '<div class="c3align">' in got)
self.assertTrue("<table>" in got)
self.assertTrue("</table>" in got)
self.assertIn("Standard Nuclear", got)
def CodonAlphabet(gc=1, include_stop_codons=False):
if isinstance(gc, (int, str)):
gc = get_code(gc)
if include_stop_codons:
motifset = list(gc.codons)
else:
motifset = list(gc.sense_codons)
motifset = [codon.upper().replace("U", "T") for codon in motifset]
a = _CodonAlphabet(motifset, moltype=DNA)
a._gc = gc
return a
def deserialise_moltype(data):
"""returns a cogent3 MolType instance, or a CodonAlphabet"""
data.pop("version", None)
label = data["moltype"]
data["moltype"] = get_moltype(label)
klass = _get_class(data.pop("type"))
if klass == _CodonAlphabet:
gc = get_code(data.pop("genetic_code"))
result = _CodonAlphabet(**data)
result._gc = gc
else:
result = data["moltype"]
return result
def __init__(self,
moltype="dna",
gc=1,
allow_rc=False,
trim_terminal_stop=True):
"""selects translatable sequences
Sequences are truncated to modulo 3. seqs.info has a translation_errors
entry.
Parameters
----------
moltype : str
molecular type, must be either DNA or RNA
gc
identifier for a genetic code or a genetic code instance
allow_rc : bool
If False, forward strand considered only. If True, and
best frame on rc, it will be negative
trim_terminal_stop : bool
exclude terminal stop codon from seqs
Returns
-------
A sequence collection. Sequences that could not be translated
are excluded.
"""
super(select_translatable, self).__init__(
input_types=self._input_types,
output_types=self._output_types,
data_types=self._data_types,
)
self._formatted_params()
moltype = get_moltype(moltype)
assert moltype.label.lower() in ("dna", "rna"), "Invalid moltype"
self._moltype = moltype
self._gc = get_code(gc)
self._allow_rc = allow_rc
self._trim_terminal_stop = trim_terminal_stop
self.func = self.get_translatable
def best_frame(seq, gc=1, allow_rc=False, require_stop=False):
"""returns reading frame start that has either no stops or a single
terminal stop codon
result will be either 1, 2, 3 (or -1, -2, -3)
Parameters
----------
gc
genetic code ID, name or instance
allow_rc
If False, forward strand considered only. If True, and
best frame on rc, it will be negative
require_stop
a terminal stop must be present
Returns
-------
int
1, 2, 3 if the best frame on the +_ strand; -1, -2, -3 if the best
frame is on the reverse strand
Raises
------
ValueError
if the minimum number of stop codons across all frames exceeds 1,
or the the stop codon is not at the sequence end
"""
gc = get_code(gc)
translations = gc.sixframes(seq)
if not allow_rc:
translations = translations[:3]
if not require_stop:
# don't count stops if they're at the end of the aa sequence
for i in range(len(translations)):
if translations[i].endswith("*"):
translations[i] = translations[i][:-1]
stops_in_frame = [(tr.count("*"), i) for i, tr in enumerate(translations)]
stops_in_frame.sort()
min_stops, frame = stops_in_frame[0]
# if min_stops > 1, cannot be translated
if min_stops > 1:
raise ValueError("%s cannot be robustly translated" % seq.name)
elif min_stops == 0 and require_stop:
# find seq with 1 stop
min_stops = 20 # nonsense value
for idx, (n, fr) in enumerate(stops_in_frame):
if n == 1:
min_stops, frame = n, fr
break
if 0 <= min_stops <= 1:
if min_stops == 1 and not translations[frame].endswith("*"):
raise ValueError("%s cannot be robustly translated" % seq.name)
else:
raise ValueError("%s cannot be robustly translated" % seq.name)
frame += 1
if allow_rc and frame > 3:
frame = 3 - frame
return frame