def test_changing_working_dir(self):
"""Mafft BaseCommand should change according to WorkingDir"""
c = Mafft(WorkingDir='/tmp/mafft_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/mafft_test','/"; ','mafft']))
c = Mafft()
c.WorkingDir = '/tmp/mafft_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/mafft_test2','/"; ','mafft']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/mafft_test')
rmdir('/tmp/mafft_test2')
def test_changing_working_dir(self):
"""Mafft BaseCommand should change according to WorkingDir"""
c = Mafft(WorkingDir='/tmp/mafft_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/mafft_test','/"; ','mafft']))
c = Mafft()
c.WorkingDir = '/tmp/mafft_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/mafft_test2','/"; ','mafft']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/mafft_test')
rmdir('/tmp/mafft_test2')
def test_base_command(self):
"""Mafft BaseCommand should return the correct BaseCommand"""
c = Mafft()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','mafft']))
c.Parameters['--quiet'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','mafft --quiet']))
c.Parameters['--globalpair'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','mafft --globalpair --quiet']))
c.Parameters['--maxiterate'].on(1000)
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ',"""mafft --maxiterate 1000 --globalpair --quiet"""]))