def __init__(
self,
amount=None,
amount_percent=None,
minimum=None,
minimum_percent=None,
location=None,
indices=None,
reference=None,
boost=1.0,
):
"""Initialize."""
# raise NotImplementedError("This class is not yet implemented")
# if location is None and (indices is not None):
# location = (min(indices), max(indices) + 1)
self.location = Location.from_data(location)
if (self.location is not None) and self.location.strand == -1:
self.location.strand = 1
self.indices = np.array(indices) if (indices is not None) else None
self.reference = reference
# self.passive_objective = passive_objective
self.amount = amount
self.amount_percent = amount_percent
self.minimum = minimum
self.minimum_percent = minimum_percent
if isinstance(amount, str) and amount.endswith("%"):
self.amount = None
self.amount_percent = float(amount[:-1])
if isinstance(minimum, str) and minimum.endswith("%"):
self.minimum = None
self.minimum_percent = float(minimum[:-1])
self.boost = boost
def __init__(
self,
location=None,
tmin=50,
tmax=70,
max_homology_length=6,
avoid_heterodim_with=None,
max_heterodim_tm=5,
avoided_repeats=((2, 5), (3, 4), (4, 3)),
):
location = Location.from_data(location)
specs = {
"unique_sequence": UniquifyAllKmers(
k=max_homology_length, location=location
),
"melting_temperature": EnforceMeltingTemperature(
mini=tmin, maxi=tmax, location=location
),
**{
"repeats_%d_%d"
% (k, n): AvoidPattern(
RepeatedKmerPattern(k, n), location=location
)
for (k, n) in avoided_repeats
},
}
if avoid_heterodim_with is not None:
specs["avoid_heterodimerization"] = AvoidHeterodimerization(
other_primers_sequences=avoid_heterodim_with,
tmax=max_heterodim_tm,
location=location,
)
self.register_specifications(specs)
def __init__(
self, stem_size=20, hairpin_window=200, location=None, boost=1.0
):
"""Initialize."""
self.stem_size = stem_size
self.hairpin_window = hairpin_window
self.location = Location.from_data(location)
self.boost = boost
def __init__(self,
species=None,
location=None,
codon_usage_table=None,
boost=1.0):
self.boost = boost
self.location = Location.from_data(location)
self.species = species
self.codon_usage_table = self.get_codons_table(species,
codon_usage_table)
def __init__(
self, pattern=None, occurences=1, location=None, center=True, boost=1.0
):
"""Initialize."""
if isinstance(pattern, str):
pattern = SequencePattern.from_string(pattern)
self.pattern = pattern
self.location = Location.from_data(location)
self.occurences = occurences
self.center = center
self.boost = boost
def __init__(self, choices=None, location=None, boost=1.0):
"""Initialize."""
choices = [
SequencePattern.from_string(c) if isinstance(c, str) else c
for c in choices
]
# PRECOMPUTE ALL VARIANTS
choices = [
variant for choice in choices for variant in choice.all_variants()
]
self.choices = choices
self.location = Location.from_data(location)
self.boost = boost
def __init__(
self,
max_edits=0,
max_edits_percent=None,
location=None,
indices=None,
target_sequence=None,
boost=1.0,
):
"""Initialize."""
if location is None and (indices is not None):
location = (min(indices), max(indices) + 1)
self.location = Location.from_data(location)
if (self.location is not None) and self.location.strand == -1:
self.location.strand = 1
self.indices = np.array(indices) if (indices is not None) else None
self.target_sequence = target_sequence
self.max_edits = max_edits
self.max_edits_percent = max_edits_percent
self.boost = boost
def __init__(self,
mini=None,
maxi=None,
target=None,
location=None,
boost=1.0):
"""Initialize."""
if isinstance(mini, str) and mini.endswith('C'):
# PROCESS CASES "45-55%" and "45%"
split = mini[:-1].split('-')
if len(split) == 2:
mini, maxi = float(split[0]), float(split[1])
else:
target = float(split[0])
if target is not None:
mini = maxi = target
else:
target = 0.5 * (mini + maxi)
self.mini = mini
self.maxi = maxi
self.target = target
self.location = Location.from_data(location)
self.boost = boost
def __init__(
self,
mini=0,
maxi=1.0,
target=None,
window=None,
location=None,
boost=1.0,
):
"""Initialize."""
if isinstance(mini, str):
mini, maxi, target, window = self.string_to_parameters(mini)
if target is not None:
mini = maxi = target
self.target = target
self.mini = mini
self.maxi = maxi
self.window = window
location = Location.from_data(location)
if location is not None and (location.strand == -1):
location = Location(location.start, location.end, 1)
self.location = location
self.boost = boost
def __init__(self, sequence=None, location=None, boost=1.0):
"""Initialize."""
self.sequence = sequence
self.location = Location.from_data(location)
self.boost = boost