def test_parameter_values(self):
infile_var = "Spellman.csv"
jobID_var = "tOut"
mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir,
jobID=jobID_var, comparison='-allPairs', cv=0.0, clumps=15, check_exist=False)
self.assertRaises(ValueError, mine.set_cv_threshold, 1.1)
self.assertRaises(ValueError, mine.set_cv_threshold, 0)
self.assertRaises(ValueError, mine.set_cv_threshold, -1)
self.assertRaises(ValueError, mine.set_cv_threshold, -2.5)
self.assertRaises(ValueError, mine.set_cv_threshold, "string")
try:
mine.set_cv_threshold("0.3")
except ValueError as e:
self.fail(e)
self.assertRaises(ValueError, mine.set_clumping_factor, 1.1)
self.assertRaises(ValueError, mine.set_clumping_factor, 0)
self.assertRaises(ValueError, mine.set_clumping_factor, -1)
self.assertRaises(ValueError, mine.set_clumping_factor, -2.5)
self.assertRaises(ValueError, mine.set_clumping_factor, "string")
try:
mine.set_clumping_factor("3")
except ValueError as e:
self.fail(e)
def test_RunMINE_run(self):
infile_var = "Spellman2.csv"
jobID_var = "tOut"
mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir,
jobID=jobID_var, comparison="-allPairs", check_exist=False)
mine.run(True)
self.assertTrue(mine.check_outfiles_with_filetag_exist(self.working_dir + infile_var + "," + jobID_var))
def test_outfile_already_exist(self):
"""
check if out file already exists,
maybe should not raise error, should
TODO: maybe it should be handle it at different way, auto rename?
"""
infile_var = "Spellman2.csv"
jobID_var = "exist"
mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir,
jobID=jobID_var, comparison="0", check_exist=False)
mine.run(debug=0)
with self.assertRaises(IOError):
RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir,
jobID=jobID_var, comparison="0", check_exist=True)
def test_RunMINE_init(self):
infile_var = "Spellman.csv"
jobID_var = "tOut"
mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir,
jobID=jobID_var, comparison='-allPairs', cv=0.0, exp=0.6, clumps=15, check_exist=False)
expected_infile = "%s%s" % (self.working_dir, infile_var)
expected_outfile = "id=%s" % jobID_var
expected = ["-jar", "MINE.jar", expected_infile, '-allPairs', "cv=0.0", "exp=0.6", "c=15", expected_outfile]
# print expected
self.assertEqual(mine.get_all_switches(), expected)
mine = RunMINE(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir,
jobID=jobID_var, comparison='-allPairs', cv=0.0, exp=0.6, clumps=15, check_exist=False,
csv_files=["f1", "f2", "f3"])
self.assertEqual([self.working_dir + "f1", self.working_dir + "f2", self.working_dir + "f3"], mine.csv_files)
def init_program(self):
# self.metasim = RunMetaSim.create_metasim_from_setting(self.setting)
if self.setting.run_mine:
self.mine = RunMINE.create_class_from_setting(self.setting)
else:
if self.setting.get("assembler_prog") is "genovo":
self.assembler = RunGenovo.create_genovo_from_setting(self.setting)
elif self.setting.get("assembler_prog") is "xgenovo":
self.assembler = RunXGenovo.create_xgenovo_from_setting(self.setting)
self.glimmer = RunGlimmer.create_glimmer_from_setting(self.setting)
# self.blast = run_BLAST.RunBlast.create_blast_from_setting(self.setting)
self.blast = RunBlast.create_blast_from_setting(self.setting)
