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("$#=0" not in stderrdata)
def test_Mafft_with_Clustalw_output(self):
"""Simple round-trip through app with clustal output"""
cmdline = MafftCommandline(mafft_exe)
#Use some properties:
cmdline.input = self.infile1
cmdline.clustalout = True
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
stdoutdata, stderrdata = cmdline()
#e.g. "CLUSTAL format alignment by MAFFT ..."
#or "CLUSTAL (-like) formatted alignment by MAFFT FFT-NS-2 (v6.240)"
self.assertTrue(stdoutdata.startswith("CLUSTAL"), stdoutdata)
self.assertTrue("$#=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
