def test_check_outfile_exist(self):
"""
check if ./MetaSim finished running, should produce 2 output files
only pass if both exist
TODO: need to check -d outfile_dir. MetaSim automatically change the filename name
"""
model_infile_var = "ErrorModelSolexa36bp.mconf"
taxon_infile_var = "MetaSim_bint.mprf"
outfile_var = "MetaSim_bint-454.20e39f4c.fna"
metasim = RunMetaSim(model_file=model_infile_var, no_reads=100,
taxon_infile=taxon_infile_var, pdir=self.data_dir, wdir=self.working_dir,
filename=outfile_var, check_exist=True)
metasim.run()
self.assertTrue(metasim.is_file_exist(self.working_dir + "MetaSim_bint-Empirical.fna"))
# test for an additional run: able to append subsequent versions?
metasim.run()
self.assertTrue(metasim.is_file_exist(self.working_dir + "MetaSim_bint-Empirical.1.fna"))
metasim.run()
self.assertTrue(metasim.is_file_exist(self.working_dir + "MetaSim_bint-Empirical.2.fna"))
os.remove(self.working_dir + "MetaSim_bint-Empirical.fna")
os.remove(self.working_dir + "MetaSim_bint-Empirical.1.fna")
os.remove(self.working_dir + "MetaSim_bint-Empirical.2.fna")
def test_RunMetaSim_run(self):
model_infile_var = "ErrorModelSolexa36bp.mconf"
taxon_infile_var = "MetaSim_bint.mprf"
outfile_var = "MetaSim_bint-Empirical"
metasim = RunMetaSim(model_file=model_infile_var, no_reads=100,
taxon_infile=taxon_infile_var, pdir=self.data_dir,
wdir=self.working_dir, filename=outfile_var, check_exist=True)
self.assertFalse(metasim.is_file_exist(self.working_dir + "test_outfile.fasta", False))
metasim.run(debug=True)
# print "7777777", self.working_dir,outfile_var
self.assertTrue(metasim.check_outfiles_with_filetag_exist(self.working_dir + outfile_var))
self.assertTrue(metasim.is_file_exist(self.working_dir + outfile_var + ".fna", True))
os.remove(self.working_dir + outfile_var + ".fna")
