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_no_reads_value(self):
model_infile_var = "ErrorModelSolexa36bp.mconf"
taxon_infile_var = "MetaSim_bint.mprf"
outfile_var = "wdir_all_reads_out.fasta"
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.assertRaises(ValueError, metasim.set_number_of_reads, 1.9)
self.assertRaises(ValueError, metasim.set_number_of_reads, -1)
self.assertRaises(ValueError, metasim.set_number_of_reads, -2.5)
self.assertRaises(ValueError, metasim.set_number_of_reads, "string")
self.assertRaises(ValueError, metasim.set_number_of_reads, "3.6")
# self.assertRaises(TypeError, metasim.set_number_of_reads, "3")
metasim.set_number_of_reads("3")
self.assertEqual(metasim.get_all_switches()[run_MetaSim.NO_READS_POSITION - 1], "-r3")
def test_init(self):
model_infile_var = "ErrorModelSolexa36bp.mconf"
taxon_infile_var = "MetaSim_bint.mprf"
outfile_var = "wdir_all_reads_out.fasta"
no_reads_var = 100
metasim = RunMetaSim(model_file=model_infile_var, no_reads=no_reads_var,
taxon_infile=taxon_infile_var, pdir=self.data_dir, wdir=self.working_dir,
filename=outfile_var, check_exist=True)
expected_model_infile = "-mg%s%s" % (self.working_dir, model_infile_var)
expected_taxon_infile = self.working_dir + taxon_infile_var
expected_no_reads = "-r%s" % no_reads_var
expected_directory = "-d%s" % self.working_dir
expected = ["cmd", expected_model_infile, expected_no_reads, expected_directory, expected_taxon_infile]
#
self.assertEqual(metasim.get_all_switches(), expected)
def test_read_outfile(self):
"""
check if it can "read" .fna
TODO: have check what happen in the file format is invalid,
assuming its the correct fasta now
"""
model_infile_var = "ErrorModelSolexa36bp.mconf"
taxon_infile_var = "MetaSim_bint.mprf"
outfile_var = "MetaSim_bint-Empirical.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()
result = metasim.read_outfile()
self.assertEqual(len(result), 2)
self.assertEqual(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 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")
def test_set_outfile_directory(self):
model_infile_var = "ErrorModelSolexa36bp.mconf"
taxon_infile_var = "MetaSim_bint.mprf"
outfile_var = "wdir_all_reads_out.fasta"
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.assertEqual(metasim.get_all_switches()[3], "-d%s" % self.working_dir)
dir_var = self.data_dir
metasim = RunMetaSim(model_file=model_infile_var, no_reads=100,
taxon_infile=taxon_infile_var, pdir=self.data_dir, wdir=dir_var,
filename=outfile_var, check_exist=False)
metasim.set_outfile_directory()
self.assertEqual(metasim.get_all_switches()[3], "-d%s" % self.data_dir)
