def GetExec(self, optList, frame):
# Respond to the "muscle" command.
self.frame = frame
plugin_exe = r"C:/Program Files (x86)/py27/Lib/site-packages/Muscle.exe"
self.outfile = r".\plugins\muscle.txt"
self.outtype = "fasta"
cline = MuscleCommandline(plugin_exe, out=self.outfile)
if '1ProfileCheck' in self.frame.paramBoxes:
if self.frame.paramBoxes['1ProfileCheck'].GetValue():
cline.profile = True
cline.in1 = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\my_seq.fasta"
cline.in2 = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\my_seq.fasta"
else:
cline.input = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\my_seq.fasta"
if '1DiagCheck' in self.frame.paramBoxes:
if self.frame.paramBoxes['1DiagCheck'].GetValue():
cline.diags = True
if "DiagLenSpin" in self.frame.paramBoxes:
cline.diaglength = int(
self.frame.paramBoxes["DiagLenSpin"])
if "DiagMargSpin" in self.frame.paramBoxes:
cline.diaglength = int(
self.frame.paramBoxes["DiagMargSpin"])
if "DiagBreakSpin" in self.frame.paramBoxes:
cline.diaglength = int(
self.frame.paramBoxes["DiagBreakSpin"])
elif "GapPenSpin" in self.frame.paramBoxes:
cline.gapopen = float(
self.frame.paramBoxes["GapPenSpin"].GetValue())
else:
cline.input = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\my_seq.fasta"
if self.frame.abet == "AA":
cline.seqtype = "protein"
elif self.frame.abet == "DNA" or self.frame.abet == "RNA":
cline.seqtype = "nucleo"
else:
cline.seqtype = "auto"
if self.frame.options:
cline.objscore = str(self.boxList[9].GetValue())
cline.weight1 = str(self.boxList[13].GetValue())
cline.weight2 = str(self.boxList[15].GetValue())
cline.anchorspacing = int(self.boxList[17].GetValue())
cline.center = float(self.boxList[19].GetValue())
cline.hydro = int(self.boxList[21].GetValue())
cline.hydrofactor = float(self.boxList[23].GetValue())
cline.maxhours = float(self.boxList[25].GetValue())
cline.maxiters = int(self.boxList[27].GetValue())
cline.maxtrees = int(self.boxList[29].GetValue())
cline.minbestcolscore = float(self.boxList[31].GetValue())
cline.minsmoothscore = float(self.boxList[33].GetValue())
cline.smoothscoreceil = float(self.boxList[35].GetValue())
cline.smoothwindow = int(self.boxList[37].GetValue())
cline.sueff = float(self.boxList[39].GetValue())
return str(cline)
def GetExec(self, optList, frame):
# Respond to the "muscle" command.
self.frame = frame
plugin_exe = r"C:/Program Files (x86)/py27/Lib/site-packages/Muscle.exe"
self.outfile=r".\plugins\muscle.txt"
self.outtype="fasta"
cline = MuscleCommandline(plugin_exe,out=self.outfile)
if '1ProfileCheck' in self.frame.paramBoxes:
if self.frame.paramBoxes['1ProfileCheck'].GetValue():
cline.profile = True
cline.in1 = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\my_seq.fasta"
cline.in2 = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\my_seq.fasta"
else:
cline.input = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\my_seq.fasta"
if '1DiagCheck' in self.frame.paramBoxes:
if self.frame.paramBoxes['1DiagCheck'].GetValue():
cline.diags=True
if "DiagLenSpin" in self.frame.paramBoxes:
cline.diaglength=int(self.frame.paramBoxes["DiagLenSpin"])
if "DiagMargSpin" in self.frame.paramBoxes:
cline.diaglength=int(self.frame.paramBoxes["DiagMargSpin"])
if "DiagBreakSpin" in self.frame.paramBoxes:
cline.diaglength=int(self.frame.paramBoxes["DiagBreakSpin"])
elif "GapPenSpin" in self.frame.paramBoxes:
cline.gapopen=float(self.frame.paramBoxes["GapPenSpin"].GetValue())
else:
cline.input=r"C:\Users\francis\Documents\Monguis\BioGui\plugins\my_seq.fasta"
if self.frame.abet=="AA":
cline.seqtype="protein"
elif self.frame.abet=="DNA" or self.frame.abet=="RNA":
cline.seqtype="nucleo"
else:
cline.seqtype="auto"
if self.frame.options:
cline.objscore=str(self.boxList[9].GetValue())
cline.weight1=str(self.boxList[13].GetValue())
cline.weight2=str(self.boxList[15].GetValue())
cline.anchorspacing=int(self.boxList[17].GetValue())
cline.center=float(self.boxList[19].GetValue())
cline.hydro=int(self.boxList[21].GetValue())
cline.hydrofactor=float(self.boxList[23].GetValue())
cline.maxhours=float(self.boxList[25].GetValue())
cline.maxiters=int(self.boxList[27].GetValue())
cline.maxtrees=int(self.boxList[29].GetValue())
cline.minbestcolscore=float(self.boxList[31].GetValue())
cline.minsmoothscore=float(self.boxList[33].GetValue())
cline.smoothscoreceil=float(self.boxList[35].GetValue())
cline.smoothwindow=int(self.boxList[37].GetValue())
cline.sueff=float(self.boxList[39].GetValue())
return str(cline)
def test_Muscle_with_options(self):
"""Round-trip through app with a switch and valued option"""
cmdline = MuscleCommandline(muscle_exe)
cmdline.set_parameter("input", self.infile1) # "input" is alias for "in"
cmdline.set_parameter("out", self.outfile2)
#Use property:
cmdline.objscore = "sp"
cmdline.noanchors = True
self.assertEqual(str(cmdline), _escape_filename(muscle_exe) +
" -in Fasta/f002" +
" -out Fasta/temp_align_out2.fa" +
" -objscore sp -noanchors")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
output, error = cmdline()
self.assertEqual(output, "")
self.assertTrue("ERROR" not in error)
self.assertTrue(error.strip().startswith("MUSCLE"), output)
def test_Muscle_with_options(self):
"""Round-trip through app with a switch and valued option"""
cmdline = MuscleCommandline(muscle_exe)
cmdline.set_parameter("input",
self.infile1) #"input" is alias for "in"
cmdline.set_parameter("out", self.outfile2)
#Use property:
cmdline.objscore = "sp"
cmdline.noanchors = True
self.assertEqual(
str(cmdline), muscle_exe + " -in Fasta/f002" +
" -out Fasta/temp_align_out2.fa" + " -objscore sp -noanchors")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
output, error = cmdline()
self.assertEqual(output, "")
self.assertTrue("ERROR" not in error)
self.assertTrue(error.strip().startswith("MUSCLE"), output)
def test_Muscle_with_options(self):
"""Round-trip through app with a switch and valued option."""
cmdline = MuscleCommandline(muscle_exe)
cmdline.set_parameter("input", self.infile1) #"input" is alias for "in"
cmdline.set_parameter("out", self.outfile2)
#Use property:
cmdline.objscore = "sp"
cmdline.noanchors = True
self.assertEqual(str(cmdline), muscle_exe +\
" -in Fasta/f002" + \
" -out Fasta/temp_align_out2.fa" + \
" -objscore sp -noanchors")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
stdin, stdout, stderr = generic_run(cmdline)
self.assertEqual(stdin.return_code, 0)
self.assertEqual(stdout.read(), "")
self.assert_("ERROR" not in stderr.read())
self.assertEqual(str(stdin._cl), str(cmdline))
def test_Muscle_with_options(self):
"""Round-trip through app with a switch and valued option"""
cmdline = MuscleCommandline(muscle_exe)
cmdline.set_parameter("input", self.infile1) #"input" is alias for "in"
cmdline.set_parameter("out", self.outfile2)
#Use property:
cmdline.objscore = "sp"
cmdline.noanchors = True
self.assertEqual(str(cmdline), muscle_exe +\
" -in Fasta/f002" + \
" -out Fasta/temp_align_out2.fa" + \
" -objscore sp -noanchors")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
child = subprocess.Popen(str(cmdline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=(sys.platform!="win32"))
output, error = child.communicate()
self.assertEqual(child.returncode, 0)
self.assertEqual(output, "")
self.assert_("ERROR" not in error)
del child
