def test_RunGlimmer_check_outfiles_exist(self):
"""
check if ./g3iterated.csh finished running, should produce 10 output files
only pass if all 10 exist
"""
infile_var = "tIn.fasta"
outfile_var = "tOut"
glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False)
is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var)
self.assertFalse(is_exist)
glimmer.run(True)
is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var)
self.assertTrue(is_exist)
# negative test, outfiles are not suppose to exist
outfile_var = "fileNotExist"
glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False)
is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var)
self.assertFalse(is_exist)
def test_RunGlimmer_run(self):
"""
with debug=True
should be able to see all 8 steps
debug - output message:
Step 1 of 8: Finding long orfs for training
Step 2 of 8: Extracting training sequences
Step 3 of 8: Building ICM
Step 4 of 8: Running first Glimmer3
Step 5 of 8: Getting training coordinates
Step 6 of 8: Making PWM from upstream regions
Step 7 of 8: Getting start-codon usage
Step 8 of 8: Running second Glimmer3
"""
infile_var = "tIn.fasta"
outfile_var = "tOut"
glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False)
is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var)
self.assertFalse(is_exist)
glimmer.run(debug=1)
is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var)
self.assertTrue(is_exist)
