def test_RunGenovo_set_infile_outfile(self):
infile_var = "test_infile.fasta"
outfile_var = "test_outfile.fasta"
genovo = RunGenovo(infile=infile_var, outfile=outfile_var,
pdir=self.data_dir, no_iter=3, thresh=250,
check_exist=False)
expected = [self.data_dir + infile_var, "3"]
self.assertEqual(genovo.assemble.get_all_switches(), expected)
expected = ["250", self.data_dir + outfile_var,
self.data_dir + infile_var + ".dump.best"]
self.assertEqual(genovo.finalize.get_all_switches(), expected)
infile_var = "test_infile2.fasta"
genovo.set_infile_name(infile_var)
self.assertEqual(genovo.assemble.get_all_switches(), [infile_var, "3"])
expected = ["250", self.data_dir + outfile_var,
infile_var + ".dump.best"]
self.assertEqual(genovo.finalize.get_all_switches(), expected)
outfile_var = "test_outfile2.fasta"
genovo.set_outfile(outfile_var)
self.assertEqual(genovo.assemble.get_all_switches(), [infile_var, "3"])
expected = ["250", outfile_var, infile_var + ".dump.best"]
self.assertEqual(genovo.finalize.get_all_switches(), expected)
def test_RunGenovo_set_number_of_iter(self):
infile_var = "test_infile.fasta"
genovo = RunGenovo(infile=infile_var, pdir=self.data_dir, no_iter=3,
thresh=250, check_exist=False)
self.assertRaises(ValueError, genovo.set_assemble_number_of_iter, 1.1)
self.assertRaises(ValueError, genovo.set_assemble_number_of_iter, -1)
self.assertRaises(ValueError, genovo.set_assemble_number_of_iter, "string")
self.assertRaises(ValueError, genovo.set_assemble_number_of_iter, "5.9")
try:
genovo.set_assemble_number_of_iter("300")
except ValueError as e:
self.fail(e)
self.assertEqual(genovo.assemble.get_all_switches()[run_genovo.ASSEMBLE_NO_ITER_POSITION - 1], "300")
def test_RunGenovo_simple_assemble(self):
infile_var = "all_read.fa"
genovo = RunGenovo(infile=infile_var, pdir=self.data_dir,
wdir=self.working_dir, no_iter=3, thresh=250,
check_exist=False)
expected = [self.working_dir + infile_var, "3"]
self.assertEqual(genovo.assemble.get_all_switches(), expected)
genovo.set_assemble_number_of_iter(10)
expected = [self.working_dir + infile_var, "10"]
self.assertEqual(genovo.assemble.get_all_switches(), expected)
infile_var = "test_infile.fasta"
genovo.set_infile_name(infile_var)
self.assertEqual(genovo.assemble.get_all_switches(), [infile_var, "10"])
def test_RunGenovo_set_cutoff(self):
"""
Note: There are different type of Errors
Feel free to change/swap/move between ValueError and TypeError
"""
infile_var = "test_infile.fasta"
genovo = RunGenovo(infile=infile_var, pdir=self.data_dir, no_iter=3,
thresh=250, check_exist=False)
self.assertRaises(ValueError, genovo.set_finalize_cutoff, 1.1)
self.assertRaises(ValueError, genovo.set_finalize_cutoff, -1)
self.assertRaises(ValueError, genovo.set_finalize_cutoff, -2.5)
self.assertRaises(ValueError, genovo.set_finalize_cutoff, "string")
try:
genovo.set_finalize_cutoff("3")
except ValueError as e:
self.fail(e)
def test_RunGenovo_simple_finalise(self):
infile_var = "test_infile.fasta"
genovo = RunGenovo(infile=infile_var, pdir=self.data_dir, no_iter=3,
thresh=250, check_exist=False)
self.assertEqual(3, len(genovo.finalize._switch))
expected = ["250", self.data_dir + "test_infile.genovo",
self.data_dir + infile_var + ".dump.best"]
self.assertEqual(genovo.finalize.get_all_switches(), expected)
genovo.set_finalize_cutoff(300)
expected = ["300", self.data_dir + "test_infile.genovo",
self.data_dir + infile_var + ".dump.best"]
self.assertEqual(genovo.finalize.get_all_switches(), expected)
infile_var = "VICTORY!!!.fasta"
genovo.set_infile_name(infile_var)
expected = ["300", self.data_dir + "test_infile.genovo",
infile_var + ".dump.best"]
self.assertEqual(genovo.finalize.get_all_switches(), expected)
def test_RunGenovo_read_finalize_outfile(self):
"""
check if it can "read" assembled contig
TODO: have check what happen in the file format is invalid,
assuming its the correct fasta now
"""
infile_var = "fIn.fasta"
outfile_var = "fOut.fasta"
genovo = RunGenovo(infile=infile_var, outfile=outfile_var,
pdir=self.data_dir, no_iter=10, thresh=250,
check_exist=False)
result = genovo.read_outfile()
self.assertEqual(len(result), 2)
self.assertEqual(list(result.keys()), ["1", "2"])
expected = [170, 60]
for i, key in enumerate(result):
# print key, i, type(result[key]), result[key]
self.assertEqual(len(result[key]), expected[i])
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)
def test_RunGenovo_run(self):
infile_var = "tIn.fasta"
outfile_var = "tOut.fasta"
genovo = RunGenovo(infile=infile_var, outfile=outfile_var,
pdir=self.data_dir, no_iter=10, thresh=100,
check_exist=True)
is_exist, _ = genovo.check_outfiles_with_filetag_exist(self.data_dir + infile_var)
self.assertFalse(is_exist)
genovo.run()
is_exist, _ = genovo.check_outfiles_with_filetag_exist(self.data_dir + infile_var)
self.assertTrue(is_exist)
self.assertTrue(genovo.is_file_exist(self.data_dir + "tOut.fasta", True))
os.remove(self.data_dir + outfile_var)
def test_RunGenovo_check_assemble_result_exist(self):
"""
check if ./assemble finished running, should produce 3 output files
only pass if all 3 exist
"""
infile_var = "assemble.fasta"
genovo = RunGenovo(infile=infile_var, pdir=self.data_dir, no_iter=10,
thresh=250, check_exist=False)
is_exist, _ = genovo.check_outfiles_with_filetag_exist(self.data_dir + infile_var)
self.assertFalse(is_exist)
genovo.run()
is_exist, _ = genovo.check_outfiles_with_filetag_exist(self.data_dir + infile_var)
self.assertTrue(is_exist)
os.remove(self.data_dir + "assemble.genovo")
# negative test, outfiles are not suppose to exist
infile_var = "fileNotExist.fasta"
genovo = RunGenovo(infile=infile_var, pdir=self.data_dir, wdir=self.working_dir, no_iter=10,
thresh=250, check_exist=False)
is_exist, _ = genovo.check_outfiles_with_filetag_exist(self.data_dir + "fileNotExist_out")
self.assertFalse(is_exist)
