def test_Mafft_with_Clustalw_output(self): """Simple round-trip through app with clustal output""" cmdline = MafftCommandline(mafft_exe) #Use some properties: cmdline.input = self.infile1 cmdline.clustalout = True self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) stdoutdata, stderrdata = cmdline() #e.g. "CLUSTAL format alignment by MAFFT ..." #or "CLUSTAL (-like) formatted alignment by MAFFT FFT-NS-2 (v6.240)" self.assertTrue(stdoutdata.startswith("CLUSTAL"), stdoutdata) self.assertTrue("$#=0" not in stderrdata)
def test_Mafft_with_Clustalw_output(self): """Simple round-trip through app with clustal output""" cmdline = MafftCommandline(mafft_exe) #Use some properties: cmdline.input = self.infile1 cmdline.clustalout = True self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) stdin, stdout, stderr = Application.generic_run(cmdline) self.assertEqual(stdin.return_code, 0) self.assert_(stdout.read().startswith("CLUSTAL format alignment by MAFFT")) self.assert_("$#=0" not in stderr.read()) self.assertEqual(str(stdin._cl), mafft_exe \ + " --clustalout Fasta/f002")
def test_Mafft_with_Clustalw_output(self): """Simple round-trip through app with clustal output""" cmdline = MafftCommandline(mafft_exe) #Use some properties: cmdline.input = self.infile1 cmdline.clustalout = True self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) result, stdout, stderr = Application.generic_run(cmdline) self.assertEqual(result.return_code, 0) output = stdout.read() #e.g. "CLUSTAL format alignment by MAFFT ..." #or "CLUSTAL (-like) formatted alignment by MAFFT FFT-NS-2 (v6.240)" self.assert_(output.startswith("CLUSTAL"), output) self.assert_("$#=0" not in stderr.read()) self.assertEqual(str(result._cl), mafft_exe \ + " --clustalout Fasta/f002")
def test_Mafft_with_Clustalw_output(self): """Simple round-trip through app with clustal output""" cmdline = MafftCommandline(mafft_exe) #Use some properties: cmdline.input = self.infile1 cmdline.clustalout = True self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) child = subprocess.Popen(str(cmdline), stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) return_code = child.wait() self.assertEqual(return_code, 0) output = child.stdout.read() #e.g. "CLUSTAL format alignment by MAFFT ..." #or "CLUSTAL (-like) formatted alignment by MAFFT FFT-NS-2 (v6.240)" self.assert_(output.startswith("CLUSTAL"), output) self.assert_("$#=0" not in child.stderr.read()) del child
def test_Mafft_with_Clustalw_output(self): """Simple round-trip through app with clustal output""" cmdline = MafftCommandline(mafft_exe) #Use some properties: cmdline.input = self.infile1 cmdline.clustalout = True self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) child = subprocess.Popen(str(cmdline), stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True, shell=(sys.platform!="win32")) stdoutdata, stderrdata = child.communicate() return_code = child.returncode self.assertEqual(return_code, 0, "Got error code %i back from:\n%s" % (return_code, cmdline)) #e.g. "CLUSTAL format alignment by MAFFT ..." #or "CLUSTAL (-like) formatted alignment by MAFFT FFT-NS-2 (v6.240)" self.assertTrue(stdoutdata.startswith("CLUSTAL"), stdoutdata) self.assertTrue("$#=0" not in stderrdata) del child