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)
