def __init__(self, min_length, location=None, extended_location=None,
include_reverse_complement=True, boost=1.0,
localization_data=None):
"""Initialize."""
self.min_length = min_length
if isinstance(location, tuple):
location = Location.from_tuple(location)
self.location = location
if isinstance(extended_location, tuple):
extended_location = Location.from_tuple(extended_location)
self.extended_location = extended_location
self.include_reverse_complement = include_reverse_complement
self.boost = 1.0
self.localization_data = localization_data
def __init__(self,
blast_db=None,
sequences=None,
word_size=4,
perc_identity=100,
num_alignments=100000,
num_threads=3,
min_align_length=20,
ungapped=True,
e_value=1e80,
culling_limit=1,
location=None):
"""Initialize."""
if isinstance(location, tuple):
location = Location.from_tuple(location)
self.blast_db = blast_db
self.sequences = sequences
self.word_size = word_size
self.perc_identity = perc_identity
self.num_alignments = num_alignments
self.num_threads = num_threads
self.min_align_length = min_align_length
self.location = location
self.e_value = e_value
self.ungapped = ungapped
self.culling_limit = culling_limit
def __init__(self, sequence=None, location=None, boost=1.0):
"""Initialize."""
self.sequence = sequence
if isinstance(location, tuple):
location = Location.from_tuple(location, default_strand=+1)
self.location = location
self.boost = boost
def __init__(self,
locations,
compatibility_condition,
condition_label='',
boost=1.0):
self.locations = [
Location.from_tuple(location) for location in locations
]
self.compatibility_condition = compatibility_condition
self.condition_label = condition_label
self.boost = boost
def __init__(self, location=None, translation=None, boost=1.0):
"""Initialize."""
self.translation = translation
if isinstance(location, tuple):
location = Location.from_tuple(location, default_strand=+1)
if (location is not None) and (location.strand not in [-1, 1]):
location = Location(location.start, location.end, 1)
self.set_location(location)
self.boost = boost
self.initialize_translation_from_problem = (translation is None)
self.initialize_location_from_problem = (location is None)
def __init__(self,
stem_size=20,
hairpin_window=200,
location=None,
boost=1.0):
"""Initialize."""
if isinstance(location, tuple):
location = Location.from_tuple(location)
self.stem_size = stem_size
self.hairpin_window = hairpin_window
self.location = location
self.boost = boost
def __init__(self,
location=None,
indices=None,
target_sequence=None,
boost=1.0):
"""Initialize."""
if isinstance(location, tuple):
location = Location.from_tuple(location)
self.location = location
self.indices = np.array(indices) if (indices is not None) else None
self.target_sequence = target_sequence
# self.passive_objective = passive_objective
self.boost = boost
def __init__(self,
max_energy=-5.0,
location=None,
optimize_initiator=False,
boost=1.0):
self.max_e = max_energy
self.boost = boost
self.optimize_initiator = optimize_initiator
if isinstance(location, tuple):
location = Location.from_tuple(location)
if location is not None and (location.strand == -1):
location = Location(location.start, location.end, 1)
self.location = location
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
if isinstance(location, tuple):
location = Location.from_tuple(location)
self.location = location
self.boost = boost
self.occurences = occurences
self.center = center
self.boost = boost
def __init__(self,
mini=0,
maxi=1.0,
target=None,
window=None,
location=None,
boost=1.0):
"""Initialize."""
if target is not None:
mini = maxi = target
self.target = target
self.mini = mini
self.maxi = maxi
self.window = window
if isinstance(location, tuple):
location = Location.from_tuple(location)
self.location = location
self.boost = boost
def __init__(self, choices=None, enzymes=None, location=None, boost=1.0):
"""Initialize."""
if enzymes is not None:
choices = [enzyme_pattern(e) for e in enzymes]
if choices is None:
raise ValueError('`choices` or `enzymes` should not be None.')
choices = [
choice if isinstance(choice, DnaNotationPattern) else
DnaNotationPattern(choice) for choice in choices
]
choices = [
variant for choice in choices for variant in choice.all_variants()
]
self.choices = choices
if isinstance(location, tuple):
location = Location.from_tuple(location, default_strand=+1)
self.location = location
self.boost = boost
def __init__(self,
pattern=None,
occurences=1,
location=None,
enzyme=None,
center=True,
boost=1.0):
"""Initialize."""
if enzyme is not None:
pattern = enzyme_pattern(enzyme)
if isinstance(pattern, str):
pattern = DnaNotationPattern(pattern)
self.pattern = pattern
if isinstance(location, tuple):
location = Location.from_tuple(location)
self.location = location
self.enzyme = enzyme
self.boost = boost
self.occurences = occurences
self.center = center
self.boost = boost