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