def test_create_blast_from_file(self):
file_var = "NotExist"
e_var = 1e-50
batch_size = 20
outfile_var = "foolname"
setting = Setting()
setting.add_all(blast_e_value=e_var, blast_wdir=self.Blast_dir,
blast_infile=file_var, blast_outfile=outfile_var,
blast_batch_size=batch_size,
)
with self.assertRaises(IOError):
RunBlast.create_blast_from_file(setting_class=setting)
infile_var = self.Blast_dir + "bIn"
setting.add("blast_infile", infile_var)
blast = RunBlast.create_blast_from_file(setting)
self.assertEqual(blast.results, dict())
self.record_index = SeqIO.index(infile_var, "fasta")
for key in self.record_index:
# print key
self.assertEqual(str(self.record_index[key].seq), str(blast.record_index[key].seq))
self.assertEqual(str(self.record_index[key].id), str(blast.record_index[key].id))
self.assertEqual(blast.e_threshold, e_var)
self.assertEqual(blast.batch_size, batch_size)
def __init__(self):
self.settings = Setting.settings()
self.handlers = Setting.handlers()
self.handlers.append(
(r"/(apple-touch-icon\.png)", web.StaticFileHandler,
dict(path=self.settings['static_path'])), )
self.setup()
print "MainApp initalize complete"
def test_Setting_set_param(self):
setting = Setting()
setting.add_all(infle="asdf", filename="zxcv", noI=2)
expected = {"infle": "asdf", "filename": "zxcv", "noI": 2}
self.assertEqual(setting.all_setting, expected)
setting.add_all(infle="asdf", outfile2="12345", noI=6)
expected = {"infle": "asdf", "filename": "zxcv",
"noI": 6, "outfile2": "12345"}
self.assertEqual(setting.all_setting, expected)
def test_missed_essential(self):
# When not all essential parameters exist, should fail.
infile = self.unittest_dir + "missedEssentials"
with self.assertRaises(KeyError):
setting = Setting.create_setting_from_file(infile)
assembler = SoftwareAssembler(setting)
def test_min_setting(self):
infile = self.unittest_dir + "testControlFileMin"
setting = Setting.create_setting_from_file(infile)
assembler = SoftwareAssembler(setting)
expected = set(TestSoftwareAssembler.list_all_parameters)
self.assertEqual(expected, set(assembler.get_all_par().viewkeys()))
print assembler.get_all_par().values()
def test_some_optional(self):
infile = self.unittest_dir + "testControlFileOp1"
setting = Setting.create_setting_from_file(infile)
assembler = SoftwareAssembler(setting)
expected = set(TestSoftwareAssembler.list_all_parameters)
self.assertEqual(expected, set(assembler.get_all_par().viewkeys()))
self.assertEqual(run_genovo.DEFAULT_GENOVO_NO_ITER, assembler.get("genovo_num_iter"))
self.assertEqual("1e-10", assembler.get("blast_e_value"))
def test_create_setting_from_file_MINE_only(self):
# When not all essential parameters exist but no optional parameters exist, should pass.
file = self.data_dir + "testControlFileMINE"
setting = Setting.create_setting_from_file(file)
expected = {
"wdir" :"/someDir/subDir/workingDir",
"mine_pdir":"/someDir/subDir/MINE",
"mine_cv":"20",
"mine_infile":"mineInfile",
"csv_files":"out1.csv,out2.csv"
}
# self.assertEqual(setting.all_setting, expected)
self.assertEqual(expected, setting.all_setting)
def test_Setting_get_glimmer(self):
setting = Setting()
setting.add_all(filename="Outfile")
# setting.print_all()
self.assertRaises(KeyError, setting.check_parameters_program, "glimmer")
setting.add_all(genovo_outfile="infile", glimmer_outfile="glimOut",
glimmer_pdir="glimp_dir", wdir=self.wdir)
expected = {"glimmer_infile": "infile", "genovo_outfile": "infile",
"filename": "Outfile", "glimmer_outfile": "glimOut",
"glimmer_pdir": "glimp_dir",
"wdir": self.wdir, "check_exist": True}
self.assertEqual(expected, setting.check_parameters_program("glimmer"))
setting.add_all(glimmer_infile="glInfile")
expected["glimmer_infile"] = "glInfile"
def test_create_setting_from_file(self):
# When not all essential parameters exist but no optional parameters exist, should pass.
file = self.data_dir + "testControlFileOp1"
setting = Setting.create_setting_from_file(file)
expected = {"wdir" :"/someDir/subDir/workingDir",
"master_tag": "genovoInfile",
"genovo_infile": "genovoInfile",
"genovo_pdir": "/someDir/subDir/genevo",
"genovo_num_iter": "20",
"glimmer_pdir":"/someDir/subDir/glimmer",
"blast_e_value":"1e-10",
}
self.assertEqual(expected, setting.all_setting)
# When not all essential parameters exist, should fail.
file = self.data_dir + "missedEssentials"
with self.assertRaises(KeyError):
Setting.create_setting_from_file(file)
# When all essential parameters exist and all optional parameters exist, should pass.
file = self.data_dir + "allPass"
try:
setting = Setting.create_setting_from_file(file)
except KeyError:
self.fail("raise KeyError unexpectedly")
# When not all essential parameters exist and some optional parameters exist, should pass.
file = self.data_dir + "testControlFileOp1"
try:
setting = Setting.create_setting_from_file(file)
except KeyError:
self.fail("raise KeyError unexpectedly")
def create_from_args(cls, args):
setting = Setting.create_setting_from_file(args)
assembler = cls(setting, args.debug)
return assembler
def test_init_program(self):
setting = Setting();
setting.add_all(genovo_infile="wdir_all_reads.fa",
genovo_pdir=self.genovo_dir)
setting.add_all(glimmer_pdir=self.glimmer_dir)
setting.add_all(wdir=self.working_dir)
# setting.add_all(metasim_model_infile="ErrorModelSolexa36bp.mconf", metasim_no_reads=10, metasim_pdir=self.metasim_dir,
# metasim_taxon_infile="MetaSim_bint.mprf")
setting.add_all(mine_pdir=self.mine_dir, mine_comparison_style="-allPairs")
setting.add_all(blast_infile="dictionary", blast_e_value=1e-15, blast_wdir=self.blast_dir, blast_outfile=None)
assembly = SoftwareAssembler(setting)
assembly.init_program()
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"
def test_Setting_get_genovo(self):
setting = Setting()
setting.add_all(assembler_infile="gInfile",
filename="gOutfile", genovo_thresh=2)
# setting.print_all()
self.assertRaises(KeyError, setting.check_parameters_program, "genovo")
setting = Setting()
setting.add_all(assembler_infile="gInfile",
filename="gOutfile", genovo_num_iter=2)
self.assertRaises(KeyError, setting.check_parameters_program, "genovo")
setting.add("genovo_thresh", 10)
setting.add_all(genovo_thresh=14, assembler_pdir="g_p_dir", wdir=self.wdir)
expected = {"assembler_infile": "gInfile", "filename": "gOutfile",
"genovo_num_iter": 2, "genovo_thresh": 14,
"assembler_pdir": "g_p_dir",
"wdir": self.wdir, "check_exist": True,
"assembler_outfile": None}
self.assertEqual(expected, setting.check_parameters_program("genovo"))
setting.add("wdir", "otherdir")
expected["wdir"] = "otherdir"
self.assertEqual(expected, setting.check_parameters_program("genovo"))
setting = Setting()
setting.add_all(assembler_infile="gInfile", genovo_thresh=14,
genovo_pdir="g_p_dir", genovo_num_iter=2)
setting.add("wdir", "otherdir")
expected.pop("filename")
self.assertEqual(expected, setting.check_parameters_program("genovo"))
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_pars(self):
setting = Setting(genovo_infile="gInfile", genovo_thresh=14)
setting.add_all(genovo_pdir="g_p_dir", genovo_num_iter=2,
wdir="otherdir", check_exist=True)
expected = {"genovo_infile": "gInfile", "genovo_num_iter": 2,
"genovo_thresh": 14, "genovo_pdir": "g_p_dir",
"check_exist": True, "genovo_outfile": None,
"wdir": "otherdir"}
print "W", setting.check_parameters_program("genovo")
self.assertEqual(expected, setting.check_parameters_program("genovo"))
setting = Setting()
setting.add_all(filename="Outfile", genovo_outfile="infile",
glimmer_outfile="glimOut", glimmer_pdir="glimp_dir",
wdir="working_dir")
expected = {"glimmer_infile": "infile", "genovo_outfile": "infile",
"filename": "Outfile", "glimmer_outfile": "glimOut",
"glimmer_pdir": "glimp_dir",
"wdir": "working_dir", "check_exist": True
}
print setting.check_parameters_program("glimmer")
self.assertEqual(expected, setting.check_parameters_program("glimmer"))
setting.add("glimmer_infile", "glInfile")
expected["glimmer_infile"] = "glInfile"
self.assertEqual(expected, setting.check_parameters_program("glimmer"))
def __init__(self):
self.settings = Setting.settings()
self.handlers = Setting.handlers()
self.handlers.append((r"/(apple-touch-icon\.png)", web.StaticFileHandler, dict(path= self.settings['static_path'])),)
self.setup()
print "MainApp initalize complete"
from core.setting import Setting st = Setting() n = st.get_setting_ip() print(n.get_port(), n.get_ip())
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"))