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
