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, 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.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
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