def GetExec(self, optList, frame):
# Respond to the "clustalw" type command.
self.frame = frame
self.boxList = optList
plugin_exe = r"C:/Program Files (x86)/ClustalW2/clustalw2.exe"
dummy = self.GetOutFile()
dummy = self.GetOutType()
cline = ClustalwCommandline(plugin_exe,infile=r".\plugins\my_seq.fasta", outfile=self.outfile)
if self.frame.abet=="AA":
cline.type="protein"
else:
cline.type="dna"
if '1PairCheck' in self.frame.paramBoxes:
if self.frame.paramBoxes['1PairCheck'].GetValue():
if '1PairwFastCheck' in sfbd:
if self.frame.paramBoxes['1PairwFastCheck'].GetValue():
if 'FastPairGapPenSpin' in self.frame.paramBoxes:
cline.pairgap = int(self.frame.paramBoxes['FastPairGapPenSpin'].GetValue())
if 'FastKTupleSpin' in self.frame.paramBoxes:
cline.ktuple = int(self.frame.paramBoxes['FastKTupleSpin'].GetValue())
if '1DiagCheck' in self.frame.paramBoxes:
if self.frame.paramBoxes['1DiagCheck'].GetValue:
if 'DFastTopDiagsSpin' in self.frame.paramBoxes:
cline.topdiags = int(self.frame.paramBoxes['DFastTopDiagsSpin'].GetValue())
if 'DFastDiagWinSpin' in self.frame.paramBoxes:
cline.window = int(self.frame.paramBoxes['DFastDiagWinSpin'].GetValue())
else:
if 'SlowPairGapPenSpin' in self.frame.paramBoxes:
cline.pwgapopen = int(self.frame.paramBoxes['SlowPairGapPenSpin'].GetValue())
if 'SlowPairGapExtPenSpin' in self.frame.paramBoxes:
cline.pwgapext = int(self.frame.paramBoxes['SlowPairGapExtPenSpin'].GetValue())
else:
if '1ProfileCheck' in self.frame.paramBoxes:
if not self.frame.paramBoxes['1ProfileCheck'].GetValue():
if 'SlowPairGapPenSpin' in self.frame.paramBoxes:
cline.gapopen = int(self.frame.paramBoxes['SlowPairGapPenSpin'].GetValue())
if 'SlowPairGapExtPenSpin' in self.frame.paramBoxes:
cline.gapext = int(self.frame.paramBoxes['SlowPairGapExtPenSpin'].GetValue())
if self.frame.options:
cline.output = str(self.boxList[1].GetValue())
cline.outorder = str(self.boxList[3].GetValue())
if '1PairCheck' in self.frame.paramBoxes:
if self.frame.paramBoxes['1PairCheck'].GetValue():
if '1PairwFastCheck' in self.frame.paramBoxes:
if self.frame.paramBoxes['1PairwFastCheck'].GetValue():
cline.score = str(self.boxList[5].GetValue())
elif self.frame.abet=="AA":
cline.pwmatrix = str(self.boxList[5].GetValue())
else:
cline.pwdnamatrix = str(self.boxList[5].GetValue())
else:
if '1ProfileCheck' in self.frame.paramBoxes:
if not self.frame.paramBoxes['1ProfileCheck'].GetValue():
if self.frame.abet=="AA":
cline.matrix = str(self.boxList[5].GetValue())
else:
cline.dnamatrix = str(self.boxList[5].GetValue())
cline.nopgap = str(self.boxList[7].GetValue())
cline.nohgap = str(self.boxList[9].GetValue())
cline.maxdiv = int(self.boxList[11].GetValue())
cline.transweight = int(self.boxList[13].GetValue())
cline.iteration = str(self.boxList[17].GetValue())
cline.numiter = int(self.boxList[15].GetValue())
return cline
