def test_Weeder(self):
""" test Weeder """
m = Weeder()
bin = locate_tool("Weeder")
if bin and self.isInstalled(bin):
(motifs, stderr, stdout) = m._run_program(bin, self.fa, ".")
self.assert_(len(motifs) > 0)
else:
sys.stderr.write("Skipping Weeder test\n")
def test_Weeder(self):
""" test Weeder """
m = Weeder()
bin = locate_tool("Weeder")
if bin and self.isInstalled(bin):
(motifs, stderr, stdout) = m.run(self.fa, ".")
self.assert_(len(motifs) > 0)
else:
sys.stderr.write("Skipping Weeder test\n")
def test_MDmodule(self):
""" test MDmodule """
m = MDmodule()
bin = locate_tool("MDmodule")
if bin and self.isInstalled(bin):
(motifs, stderr, stdout) = m._run_program(bin, self.fa, ".")
#print motifs
self.assert_(len(motifs) > 0)
else:
sys.stderr.write("Skipping MDmodule test\n")
def test_MotifSampler(self):
""" test MotifSampler """
m = MotifSampler()
bin = locate_tool("MotifSampler")
if bin and self.isInstalled(bin):
(motifs, stderr, stdout) = m.run(self.fa, ".", {"background":os.path.join(self.data_dir, "test.bg")})
#print motifs
self.assert_(len(motifs) > 0)
else:
sys.stderr.write("Skipping MotifSampler test\n")
def test_MDmodule(self):
""" test MDmodule """
m = MDmodule()
bin = locate_tool("MDmodule")
if bin and self.isInstalled(bin):
(motifs, stderr, stdout) = m.run(self.fa, ".")
#print motifs
self.assert_(len(motifs) > 0)
else:
sys.stderr.write("Skipping MDmodule test\n")
def test_meme(self):
""" test meme """
m = Meme()
bin = locate_tool("Meme")
if bin and self.isInstalled(bin):
(motifs, stderr, stdout) = m.run(self.fa, ".")
#print "meme:", motifs
self.assert_(len(motifs) > 0)
else:
sys.stderr.write("Skipping meme test\n")
def test_MotifSampler(self):
""" test MotifSampler """
m = MotifSampler()
bin = locate_tool("MotifSampler")
if bin and self.isInstalled(bin):
(motifs, stderr, stdout) = m._run_program(
bin, self.fa, ".",
{"background": os.path.join(self.data_dir, "test.bg")})
#print motifs
self.assert_(len(motifs) > 0)
else:
sys.stderr.write("Skipping MotifSampler test\n")
