def errorCheck(self): err = [] #check possible errors nt = [ 'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', '*' ] for seq in self.sequences: for letter in seq: if (letter not in nt): err.append("Sequence contains invalid letter: " + letter) try: self.scoringMatrix = FileReader.ScoringMatrix( self, self.Scoring_Function) except FileNotFoundError: err.append("file is not found: " + self.Scoring_Function) except IOError: err.append("file cannot be opened: " + self.Scoring_Function) if (len(err) == 0): self.errors = None else: self.errors = "\n".join(err) return err
def errorCheck(self): errors = [] if not isinstance(self.Gap_Penalty, int): errors.append("Gap cost value should be integer") nt = ['A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', '*'] for seq in self.seq1: for letter in seq: if (letter not in nt): errors.append("Sequence contains invalid letter: " + letter) nt = ['A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', '*'] for seq in self.seq2: for letter in seq: if (letter not in nt): errors.append("Sequence contains invalid letter: " + letter) try: self.scoringMatrix = FileReader.ScoringMatrix(self, self.Scoring_Matrix) except FileNotFoundError: errors.append("file is not found: " + self.Scoring_Matrix) except IOError: errors.append("file cannot be opened: " + self.Scoring_Matrix) if (len(errors) == 0): self.errors = None else: self.errors = "\n".join(errors) return errors
def errorCheck(self): errors = [] if not isinstance(self.gapPenality, int): errors.append("Gap cost value should be integer") if not isinstance(self.gapExtended, int): errors.append("Gap extension value should be integer") try: self.scoringMatrix = FileReader.ScoringMatrix(self, self.IP_Matrix) except FileNotFoundError: errors.append("file is not found: " + filename) except IOError: errors.append("file cannot be opened: " + filename) except ValueError as Err: errors.append("values are not integer: " + Err) except: err = sys.exc_info()[0] errors.append("Error: " + str(err)) if (len(errors) == 0): self.errors = "0" else: self.errors = "\n".join(errors)
def ComputeScore(self, alignment=None): errors = [] try: self.file = FileReader.ScoringMatrix(self, self.Scoring_Function) except FileNotFoundError: errors.append("file is not found: " + self.Scoring_Function) except IOError: errors.append("file cannot be opened: " + self.Scoring_Function) if (len(errors) == 0): self.errors = None self.file = FileReader.ScoringMatrix(self, self.Scoring_Function) else: self.errors = "\n".join(errors) SOP = 0 i = 1 for seqA in alignment: for seqB in alignment[i:]: Score = 0 for j in range(len(seqA)): SequenceA = seqA[j] SequenceB = seqB[j] SequenceA = SequenceA.replace('-', '*') SequenceB = SequenceB.replace('-', '*') Score += int(self.file[SequenceA][SequenceB]) SOP += Score i += 1 return SOP
def nw(self): self.scoringMatrix = FileReader.ScoringMatrix(self, self.Scoring_Matrix) self.Filled_Matrix= self.Matrix_Filling() self.Aligned_Sequence = self.Traceback() return self.Aligned_Sequence
def gotoh(self): self.scoringMatrix = FileReader.ScoringMatrix(self, self.IP_Matrix) self.filledMatrices = self.matrixFilling() self.alignedSequence = self.Traceback() return self.alignedSequence