def test_raxml_params(self):
"""raxml should raise exception if missing required params"""
r = Raxml(WorkingDir="/tmp")
r.SuppressStdout = True
r.SuppressStderr = True
# raise error by default
self.assertRaises(ValueError, r)
# specify output name
r.Parameters['-n'].on("test_name")
r.Parameters["-p"].on(randint(1, 100000))
self.assertRaises(ApplicationError, r)
# specify model
r.Parameters['-m'].on("GTRCAT")
self.assertRaises(ApplicationError, r)
r.Parameters['-s'].on(self.test_fn1)
self.assertRaises(ApplicationError, r)
self.writeTmp(self.test_fn1)
o = r()
o.cleanUp()
remove(self.test_fn1)
def test_raxml_params(self):
"""raxml should raise exception if missing required params"""
r = Raxml(WorkingDir="/tmp")
r.SuppressStdout = True
r.SuppressStderr = True
# raise error by default
self.assertRaises(ValueError, r)
# specify output name
r.Parameters['-n'].on("test_name")
r.Parameters["-p"].on(randint(1,100000))
self.assertRaises(ApplicationError, r)
# specify model
r.Parameters['-m'].on("GTRCAT")
self.assertRaises(ApplicationError, r)
r.Parameters['-s'].on(self.test_fn1)
self.assertRaises(ApplicationError, r)
self.writeTmp(self.test_fn1)
o = r()
o.cleanUp()
remove(self.test_fn1)
def test_raxml_from_file(self):
"""raxml should run correctly using filename"""
r = Raxml(WorkingDir="/tmp")
r.Parameters['-s'].on(self.test_fn1)
r.Parameters['-m'].on("GTRCAT")
r.Parameters['-n'].on("test_me")
r.Parameters["-p"].on(randint(1, 100000))
# test with abs filename
cur_out = self.test_fn1
self.writeTmp(cur_out)
out = r()
out.cleanUp()
remove(cur_out)
# test with rel + working dir
r.Parameters['-s'].on(self.test_fn2)
r.Parameters['-n'].on("test_me2")
r.Parameters['-w'].on("/tmp/")
r.Parameters["-p"].on(randint(1, 100000))
self.writeTmp(self.test_fn1)
out = r()
out.cleanUp()
remove(self.test_fn1)
r.Parameters['-s'].on("\"%s\"" % self.test_fn1_space)
r.Parameters['-n'].on("test_me3")
r.Parameters['-w'].on("/tmp/")
r.Parameters["-p"].on(randint(1, 100000))
#print r.BaseCommand
self.writeTmp(self.test_fn1_space)
out = r()
out.cleanUp()
remove(self.test_fn1_space)
def test_raxml(self):
"""raxml BaseCommand should return the correct BaseCommand"""
r = Raxml()
self.assertEqual(r.BaseCommand, \
''.join(['cd \"',getcwd(),'/\"; ','raxmlHPC -f d -# 1']))
r.Parameters['-s'].on('seq.nexus')
self.assertEqual(r.BaseCommand,\
''.join(['cd \"',getcwd(),'/\"; ',\
'raxmlHPC -f d -s seq.nexus -# 1']))