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)