def __init__(
self,
hiObject=None,
solution=None,
label="",
args={
'hi_range': (0, 59),
'mutable_region': None,
'cds_region': None,
'keep_aa': True
}):
if hiObject == None: #create new instance
#General properties of feature
Feature.__init__(self, solution=solution, label=label)
#Specifics of this Feature
self.hi_range = args['hi_range']
self.sequence = solution.sequence[self.hi_range[0]:(
self.hi_range[1] + 1)]
self.mutable_region = args[
'mutable_region'] if 'mutable_region' in args else solution.mutable_region
self.cds_region = args[
'cds_region'] if 'cds_region' in args else solution.cds_region
self.keep_aa = args[
'keep_aa'] if 'keep_aa' in args else solution.keep_aa
self.set_scores()
self.set_level()
else: #copy instance
Feature.__init__(self, hiObject)
self.hi_range = hiObject.hi_range
self.sequence = hiObject.sequence
self.mutable_region = hiObject.mutable_region
self.cds_region = hiObject.cds_region
self.keep_aa = hiObject.keep_aa
self.codons_hi = hiObject.codons_hi
self.scores = hiObject.scores
def __init__(self,
bottleneckObject=None,
solution=None,
label="",
args={
'bottleneck_range': (0, 59),
'mutable_region': None,
'keep_aa': True
}):
if bottleneckObject == None: #create new instance
#General properties of feature
Feature.__init__(self, solution=solution, label=label)
#Specifics of this Feature
self.bottleneck_range = args['bottleneck_range']
self.sequence = solution.sequence[self.bottleneck_range[0]:self.
bottleneck_range[1] + 1]
self.mutable_region = args[
'mutable_region'] if 'mutable_region' in args else solution.mutable_region
self.cds_region = args[
'cds_region'] if 'cds_region' in args else solution.cds_region
self.keep_aa = args[
'keep_aa'] if 'keep_aa' in args else solution.keep_aa
self.set_scores()
self.set_level()
self.calculate_mutable_segments()
else: #copy instance
Feature.__init__(self, bottleneckObject)
self.bottleneck_range = bottleneckObject.bottleneck_range
self.sequence = bottleneckObject.sequence
self.mutable_region = bottleneckObject.mutable_region
self.keep_aa = bottleneckObject.keep_aa
self.segmentMutation = bottleneckObject.segmentMutation
self.bot_scores = bottleneckObject.bot_scores
self.bot_smooth = bottleneckObject.bot_smooth
self.scores = bottleneckObject.scores
def __init__(self, structureObject = None, solution = None, label="", args = { 'structure_range' : (0,59),
'mutable_region' : None,
'cds_region' : None,
'keep_aa' : True }):
if structureObject == None: #create new instance
#General properties of feature
Feature.__init__(self, solution=solution, label=label)
#Specifics of this Feature
self.structurefile = solution.solid + label
self.structure_range = args['structure_range']
logger.debug('RNA range set to: {}:{}'.format(self.structure_range[0], self.structure_range[1]))
self.sequence = solution.sequence[self.structure_range[0]:self.structure_range[1]]
self.mutable_region = args['mutable_region'] if 'mutable_region' in args else solution.mutable_region
self.cds_region = args['cds_region'] if 'cds_region' in args else solution.cds_region
self.keep_aa = args['keep_aa'] if 'keep_aa' in args else solution.keep_aa
self.set_scores()
self.set_level()
else: #copy instance
Feature.__init__(self, featureObject=structureObject)
self.structurefile = structureObject.structurefile
self.structure_range = structureObject.structure_range
self.sequence = structureObject.sequence
self.mutable_region = structureObject.mutable_region
self.cds_region = structureObject.cds_region
self.keep_aa = structureObject.keep_aa
self.scores = structureObject.scores
def __init__(
self,
structureObject=None,
solution=None,
label="",
args={
'structure_range': (0, 59),
'acc_region': [],
'window': 50,
'mutable_region': None,
'cds_region': None,
'keep_aa': True
}):
#General properties of feature
Feature.__init__(self, solution=solution, label=label)
#Specifics of this Feature
self.structurefile = solution.solid + label
self.structure_range = args['structure_range']
self.acc_region = args['acc_region'] if 'acc_region' in args else []
self.window = args['window'] if 'window' in args else 50
self.sequence = solution.sequence[self.structure_range[0]:self.
structure_range[1]]
self.mutable_region = args[
'mutable_region'] if 'mutable_region' in args else solution.mutable_region
self.cds_region = args[
'cds_region'] if 'cds_region' in args else solution.cds_region
self.keep_aa = args[
'keep_aa'] if 'keep_aa' in args else solution.keep_aa
self.set_scores()
self.set_level()
def __init__(self, window_size=50,
featureObject=None,
solution=None,
label="",
args={'feature_range' : (0, 59),
'mutable_region': None,
'cds_region' : None,
'keep_aa' : True}):
if featureObject == None: # create new instance
# General properties of feature
Feature.__init__(self, solution=solution, label=label)
# Specifics of this Feature
self.window_size = window_size
self.feature_range = args['feature_range']
self.sequence = solution.sequence[self.feature_range[0]:self.feature_range[1]]
self.mutable_region = args['mutable_region'] if 'mutable_region' in args else solution.mutable_region
self.cds_region = args['cds_region'] if 'cds_region' in args else solution.cds_region
self.keep_aa = args['keep_aa'] if 'keep_aa' in args else solution.keep_aa
self.set_scores()
self.set_level()
else: # copy instance
Feature.__init__(self, featureObject)
self.feature_range = featureObject.feature_range
self.sequence = featureObject.sequence
self.mutable_region = featureObject.mutable_region
self.cds_region = featureObject.cds_region
self.keep_aa = featureObject.keep_aa
self.scores = featureObject.scores
self.window_start_index = 0
def __init__(
self,
nucleotideContentObject=None,
solution=None,
label="",
args={
'ntcontent_range': (0, 9),
'mutable_region': None,
'cds_region': None,
'keep_aa': True
}):
if nucleotideContentObject == None: #create new instance
#General properties of feature
Feature.__init__(self, solution=solution, label=label)
#Specifics of this Feature
self.ntcontent_range = args['ntcontent_range']
self.sequence = solution.sequence[self.ntcontent_range[0]:self.
ntcontent_range[1] + 1]
self.mutable_region = args[
'mutable_region'] if 'mutable_region' in args else solution.mutable_region
self.cds_region = args[
'cds_region'] if 'cds_region' in args else solution.cds_region
self.keep_aa = args[
'keep_aa'] if 'keep_aa' in args else solution.keep_aa
self.set_scores()
self.set_level()
else:
Feature.__init__(self, nucleotideContentObject)
self.ntcontent_range = nucleotideContentObject.ntcontent_range
self.sequence = nucleotideContentObject.sequence
self.mutable_region = nucleotideContentObject.mutable_region
self.cds_region = nucleotideContentObject.cds_region
self.keep_aa = nucleotideContentObject.keep_aa
self.scores = nucleotideContentObject.scores
def __init__(self,
duplexObject=None,
solution1=None,
solution2=None,
label="",
args={
'rnaMolecule1region': None,
'rnaMolecule2region': None
}):
if duplexObject == None:
#General properties of feature
Feature.__init__(self, solution=solution1, label=label)
#Specifics of this Feature
self.solution = solution1
self.solution2 = solution2
self.duplexFile = str(solution1.solid) + '-' + str(
solution2.solid) + label
self.rnaMolecule1region = args['rnaMolecule1region']
self.rnaMolecule1seq = self.solution.sequence[
self.rnaMolecule1region[0]:(self.rnaMolecule1region[1] + 1)]
self.mutable_region = args[
'mutable_region1'] if 'mutable_region1' in args else None
self.cds_regions = args[
'cds_regions1'] if 'cds_regions1' in args else None
self.keep_aa = args['keep_aa1'] if 'keep_aa1' in args else False
self.rnaMolecule2region = args['rnaMolecule2region']
self.rnaMolecule2seq = self.solution2.sequence[
self.rnaMolecule2region[0]:(self.rnaMolecule2region[1] + 1)]
self.mutable_region2 = args[
'mutable_region2'] if 'mutable_region2' in args else None
self.cds_regions2 = args[
'cds_regions2'] if 'cds_regions2' in args else None
self.keep_aa2 = args['keep_aa2'] if 'keep_aa2' in args else False
self.set_scores()
self.set_level()
else:
#General properties of feature
Feature.__init__(self, duplexObject)
#Specifics of this Feature
self.solution = duplexObject.solution
self.solution2 = duplexObject.solution2
self.duplexFile = duplexObject.duplexFile
self.rnaMolecule1region = duplexObject.rnaMolecule1region
self.rnaMolecule1seq = duplexObject.rnaMolecule1seq
self.mutable_region = duplexObject.mutable_region
self.cds_regions = duplexObject.cds_regions
self.keep_aa = duplexObject.keep_aa
self.rnaMolecule2region = duplexObject.rnaMolecule2region
self.rnaMolecule2seq = duplexObject.rnaMolecule2seq
self.mutable_region2 = duplexObject.mutable_region2
self.cds_regions2 = duplexObject.cds_regions2
self.keep_aa2 = duplexObject.keep_aa2
self.scores = duplexObject.scores
def __init__(
self,
motifObject=None,
solution=None,
label="",
args={
'pwm': None,
'motif_range': (0, 9),
'mutable_region': None,
'cds_region': None,
'keep_aa': True
}):
if motifObject == None: #create new instance
#General properties of feature
Feature.__init__(self, solution=solution, label=label)
#Specifics of this Feature
self.pwm = args['pwm']
self.motif_range = args['motif_range']
self.sequence = solution.sequence[self.motif_range[0]:self.
motif_range[1] + 1]
self.mutable_region = [
i - self.motif_range[0] for i in
set(range(self.motif_range[0], self.motif_range[1] + 1))
& set(args['mutable_region'])
] if 'mutable_region' in args else solution.mutable_region
self.cds_region = args[
'cds_region'] if 'cds_region' in args else solution.cds_region
self.keep_aa = args[
'keep_aa'] if 'keep_aa' in args else solution.keep_aa
self.set_scores()
self.set_level()
else: #copy instance
Feature.__init__(self,
solution=motifObject.solution,
label=motifObject.label)
self.pwm = motifObject.pwm
self.motif_range = motifObject.motif_range
self.sequence = motifObject.sequence
self.mutable_region = motifObject.mutable_region
self.cds_region = motifObject.cds_region
self.keep_aa = motifObject.keep_aa
self.scores = motifObject.scores
def mutate(self):
return Feature.randomMutation(self, mutable_region=self.mutable_region)