Esempio n. 1
0
    def randomMutation(
            self,
            pos=None,
            n_mut=[1, 1, 1, 1, 2, 2, 2, 2, 3, 4, 5, 6, 20, 30, 50, 100, 200],
            mutable_region=None):
        if mutable_region == None:
            if self.mutable_region == None:
                mutable_region = self.solution.mutable_region
            else:
                mutable_region = self.mutable_region

        logger.debug('Mutable region: {}'.format(mutable_region))

        new_seq = Functions.randomMutationOperator(
            self.solution.sequence,
            self.solution.keep_aa,
            mutable_region,
            self.solution.cds_region,
            cai_table=self.solution.cai_table,
            pos=pos,
            n_mut=n_mut)

        return Solution.Solution(sol_id=str(uuid4().int),
                                 sequence=new_seq,
                                 project_dir=self.solution.project_dir,
                                 cds_region=self.solution.cds_region,
                                 keep_aa=self.solution.keep_aa,
                                 mutable_region=self.solution.mutable_region,
                                 parent=self.solution,
                                 design=self.solution.designMethod)
Esempio n. 2
0
 def set_scores(self,
                scoring_function=Functions.analyze_duplex_mfe_rnafold):
     self.scores.update(
         Functions.appendLabelToDict(
             scoring_function(filename=self.duplexFile,
                              project_dir=self.solution.project_dir),
             self.label))
Esempio n. 3
0
 def set_scores(self,
                scoring_function=Functions.analyze_duplex_structure_rnafold
                ):
     self.scores.update(
         Functions.appendLabelToDict(
             scoring_function(seq1=self.rnaMolecule1seq,
                              seq2=self.rnaMolecule2seq,
                              filename=self.duplexFile,
                              project_dir=self.solution.project_dir),
             self.label))
Esempio n. 4
0
 def set_scores(self, scoring_function=Functions.analyze_duplex_structure):
     self.scores.update(
         Functions.appendLabelToDict(
             scoring_function(self.rnaMolecule1seq, self.rnaMolecule2seq,
                              self.duplexFile), self.label))
     pass
Esempio n. 5
0
 def set_scores(self, scoring_function=Functions.analyze_duplex_mfe):
     self.scores.update(
         Functions.appendLabelToDict(scoring_function(self.duplexFile),
                                     self.label))
Esempio n. 6
0
 def set_scores(self, scoring_function=Functions.analyze_pwm_score):
     self.scores = Functions.appendLabelToDict(
         scoring_function(self.sequence, self.pwm), self.label)
Esempio n. 7
0
 def set_scores(self, scoring_function=Functions.analyze_structure_prob):
     #compute structure
     self.scores.update(
         Functions.appendLabelToDict(
             scoring_function(self.sequence, self.structurefile,
                              self.window, self.acc_region), self.label))
Esempio n. 8
0
 def set_scores(self, scoring_function=Functions.analyze_structure_ds):
     self.scores.update(
         Functions.appendLabelToDict(scoring_function(self.structurefile),
                                     self.label))
Esempio n. 9
0
 def set_scores(self, scoring_function=Functions.analyze_structure_mfe):
     self.scores.update(
         Functions.appendLabelToDict(
             scoring_function(filename=self.structurefile,
                              project_dir=self.solution.project_dir),
             self.label))
 def set_scores(self, scoring_function=Functions.analyze_ntcontent):
     self.scores = Functions.appendLabelToDict(
         scoring_function(self.sequence), self.label)
Esempio n. 11
0
    def validateSolution(self, solution):
        '''
        Solution validation tests
        '''
        return True
        
        if solution.sequence == None:
            return 0
        
        valid = True
        e_type=None
      
        variable_region = solution.sequence[solution.mutable_region[0]:(solution.mutable_region[-1]+1)]
                
        #No Promoters
        promoter_putative_region = solution.sequence[(solution.mutable_region[0]-30):(solution.mutable_region[-1]+31)]
        (score, position, spacer) = Functions.look_for_promoters(promoter_putative_region)
        if score >= 0.3990166: #0.95 percentile for Promoter PWM scores
            valid = False
            position = (solution.mutable_region[0]-30) + position
            e_type = "prom"
            sys.stderr.write("SolutionValidator: High Promoter score\n")
                
        #No RBS
        rbs_putative_region = solution.sequence[(solution.mutable_region[0]-12):(solution.mutable_region[-1]+11)]
        (score, position) = Functions.look_for_RBS(rbs_putative_region)
        if score >= 0.820515: #0.95 percentile for RBS PWM scores
            valid = False
            position = (solution.mutable_region[0]-12) + position
            e_type = "rbs"      
            sys.stderr.write("SolutionValidator: High RBS score: "+str(score)+" - "+str(position)+"\n")    
        
        #No Terminator
        term_putative_region = solution.sequence[(solution.mutable_region[0]-30):(solution.mutable_region[-1]+31)]
        score = Functions.look_for_terminators(term_putative_region)
        if score >= 90: #90% confidence from transtermHP
            e_type = "term"
            valid = False
            sys.stderr.write("SolutionValidator: High Terminator score\n")    
        
        #No stop codon
        for i in range(0,len(variable_region),3):
            if codon2aa_table[variable_region[i:i+3]]=='stop':
                sys.stderr.write("SolutionValidator: Stop codon found\n")
                e_type = "stopcodon"
                valid = False
                position = solution.mutable_region[0]+i
                break            
                    
        #No restriction enzymes
        rsite_putative_region = solution.sequence[(solution.mutable_region[0]-6):(solution.mutable_region[-1])]
        if 'ggtacc' in rsite_putative_region:
            e_type = "rsite"
            sys.stderr.write("SolutionValidator: Restriction enzyme found\n")
            position = (solution.mutable_region[0]-6)+rsite_putative_region.index('ggtacc')
            valid = False
        
        if 'ggatcc' in rsite_putative_region:
            e_type = "rsite"
            sys.stderr.write("SolutionValidator: Restriction enzyme found\n")
            position = (solution.mutable_region[0]-6)+rsite_putative_region.index('ggatcc')
            valid = False                
            
        #No bases run of more than 5nt
        repeat_putative_region = solution.sequence[(solution.mutable_region[0]-6):(solution.mutable_region[-1]+7)]
        for b_run in ('aaaaaa','tttttt','gggggg','cccccc'):
            if b_run in repeat_putative_region:
                sys.stderr.write("SolutionValidator: Bases run for more than 5 found\n")            
                valid = False
                position = (solution.mutable_region[0]-6) + repeat_putative_region.index(b_run)
                e_type = "repeats"


        solution.valid = valid
                
        if valid == True:
            return (valid,None,None)
        else:
            return (valid,position,e_type)