def GetExec(self, optList, frame):
# Respond to the "embossn" type command.
self.frame = frame
plugin_exe = r"C:/mEMBOSS/water.exe"
self.outfile = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\water.txt"
self.outtype = "fasta"
cline = WaterCommandline(plugin_exe, asequence=str(self.frame.paramBoxes[1].GetValue()), bsequence=str(self.frame.paramBoxes[3].GetValue()))
cline.outfile = self.outfile
cline.gapopen = self.param[7].GetValue()
cline.gapextend = self.param[9].GetValue()
if self.param[10].GetValue():
cline.similarity = True
else:
cline.similarity = False
if self.frame.abet=="AA":
cline.snucleotide = True
cline.sprotein = False
elif self.frame.abet=="DNA" or self.frame.abet=="RNA":
cline.snucleotide = True
cline.sprotein = False
if self.frame.options:
t = self.boxList[3].GetValue()
if t != '':
cline.datafile = str(t)
return str(cline)
def GetExec(self, optList, frame):
# Respond to the "embossn" type command.
self.frame = frame
plugin_exe = r"C:/mEMBOSS/water.exe"
self.outfile = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\water.txt"
self.outtype = "fasta"
cline = WaterCommandline(
plugin_exe,
asequence=str(self.frame.paramBoxes[1].GetValue()),
bsequence=str(self.frame.paramBoxes[3].GetValue()))
cline.outfile = self.outfile
cline.gapopen = self.param[7].GetValue()
cline.gapextend = self.param[9].GetValue()
if self.param[10].GetValue():
cline.similarity = True
else:
cline.similarity = False
if self.frame.abet == "AA":
cline.snucleotide = True
cline.sprotein = False
elif self.frame.abet == "DNA" or self.frame.abet == "RNA":
cline.snucleotide = True
cline.sprotein = False
if self.frame.options:
t = self.boxList[3].GetValue()
if t != '':
cline.datafile = str(t)
return str(cline)
