def test_Setting_get_blast(self):
setting = Setting()
setting.add_all(blast_infile="bInfile", blast_outfile="bOutfile")
with self.assertRaises(KeyError):
setting.check_parameters_program("blast")
setting.add_all(blast_e_value=1e-15,
wdir="working_dir", check_exist=True)
expected = {"blast_infile": "bInfile", "blast_outfile": "bOutfile",
"blast_e_value": 1e-15, "blast_batch_size": 20,
"wdir": "working_dir", "check_exist": True
}
setting.debug = True
self.assertEqual(expected, setting.check_parameters_program("blast"))
setting.add("wdir", "otherdir")
expected["wdir"] = "otherdir"
self.assertEqual(expected, setting.check_parameters_program("blast"))
setting = Setting()
setting.add_all(blast_infile="bInfile")
setting.add("wdir", "otherdir")
setting.add("blast_e_value", 1e-15)
setting.add("blast_outfile", "bOutfile")
# expected.pop("filename")
# TODO: debug switch
setting.debug = True
self.assertEqual(expected, setting.check_parameters_program("blast"))
def test_Setting_get_metasim(self): # "metasim_pdir", "metasim_model_infile", "metasim_taxon_infile", "metasim_no_reads"
setting = Setting()
setting.add_all(metasim_model_infile="mmInfile",
filename="mOutfile", metasim_no_reads=200)
# setting.print_all()
self.assertRaises(KeyError, setting.check_parameters_program, "metasim")
setting = Setting()
setting.add_all(metasim_model_infile="mmInfile",
filename="mOutfile", metasim_taxon_infile="tInfile")
self.assertRaises(KeyError, setting.check_parameters_program, "metasim")
setting.add("metasim_pdir", "m_p_dir")
setting.add_all(metasim_no_reads=250, wdir=self.wdir)
expected = {"metasim_model_infile": "mmInfile", "filename": "mOutfile",
"metasim_taxon_infile": "tInfile", "metasim_pdir": "m_p_dir",
"metasim_no_reads": 250,
"wdir": self.wdir, "check_exist": True,
"metasim_outfile": None}
setting.debug = 0
self.assertEqual(expected, setting.check_parameters_program("metasim"))
setting.add("wdir", "otherdir")
expected["wdir"] = "otherdir"
self.assertEqual(expected, setting.check_parameters_program("metasim"))
setting = Setting()
setting.add_all(metasim_model_infile="mmInfile", metasim_no_reads=250,
metasim_taxon_infile="tInfile", metasim_pdir="m_p_dir")
setting.add("wdir", "otherdir")
expected.pop("filename")
self.assertEqual(expected, setting.check_parameters_program("metasim"))
def test_Setting_get_mine(self):
setting = Setting()
setting.add_all(filename="Outfile")
setting.debug = True
# setting.print_all()
# self.assertRaises(KeyError, setting._get_mine())
setting.add_all(mine_outfile="mineOut",
mine_pdir="mine_pdir", mine_comparison_style="-allPairs")
setting.add("mine_infile", "infile")
setting.add("wdir", "working_dir")
setting.add("csv_files", "file1,file2,file3")
expected = {"mine_infile": "infile",
"filename": "Outfile", "mine_outfile": "mineOut",
"mine_pdir": "mine_pdir", "mine_comparison_style": "-allPairs",
"wdir": "working_dir", "check_exist": True,
"mine_cv": 0.0, "mine_exp": 0.6,
"mine_clumps": 15, "mine_jobID": None,
"csv_files": ["file1", "file2", "file3"]}
self.assertEqual(expected, setting.check_parameters_program("mine"))
setting.add_all(mine_infile="mineInfile")
expected["mine_infile"] = "mineInfile"
