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_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_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)