def test_RunGlimmer_set_infile_outfile(self): infile_var = "test_infile.fasta" outfile_var = "test_outfile.fasta" glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) expected = ([self.data_dir + infile_var, self.data_dir + "test_outfile.fasta"], [self.data_dir + infile_var, self.data_dir + "test_outfile.fasta.predict"]) self.assertEqual(glimmer.get_all_switches(), expected) # orf_var = "testORF" # glimmer = RunGlimmer(infile=infile_var, filename=outfile_var, orfs=orf_var, pdir=self.data_dir, check_exist=False) # self.assertEqual(3, len(glimmer.get_switch())) # self.assertEqual(glimmer.get_switch(), [self.data_dir + infile_var, self.data_dir + outfile_var, # self.data_dir + orf_var]) infile_var = "test_infile2.fasta" glimmer.set_infile_name(infile_var) expected = ([ infile_var, self.data_dir + "test_outfile.fasta"], [ infile_var, self.data_dir + "test_outfile.fasta.predict"]) self.assertEqual(glimmer.get_all_switches(), expected) outfile_var = "test_outfile2.fasta" glimmer.set_outfile(outfile_var) expected = ([ infile_var, "test_outfile2.fasta"], [ infile_var, "test_outfile2.fasta.predict"]) self.assertEqual(glimmer.get_all_switches(), expected)
def test_RunGlimmer_init(self): infile_var = "all_reads.fa" test_glimmer = RunGlimmer(infile_var, pdir=self.data_dir, check_exist=False) expected = [self.data_dir + infile_var, self.data_dir + "all_reads.glimmer"] self.assertEqual(test_glimmer.get_all_switches()[0], expected) expected = [self.data_dir + infile_var, self.data_dir + "all_reads.glimmer.predict"] self.assertEqual(test_glimmer.get_all_switches()[1], expected)
def test_RunGlimmer_set_outfile(self): infile_var = "test_infile.fasta" outfile_var = "testOutfile" extract = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) expected = ([self.data_dir + infile_var, self.data_dir + "testOutfile"], [self.data_dir + infile_var, self.data_dir + "testOutfile.predict"]) self.assertEqual(extract.get_all_switches(), expected) infile_var = "test_infile.xyz.fasta.abc" extract = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) expected = ([self.data_dir + infile_var, self.data_dir + "testOutfile"], [self.data_dir + infile_var, self.data_dir + "testOutfile.predict"]) self.assertEqual(extract.get_all_switches(), expected) infile_var = "test_infile" extract = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) expected = ([self.data_dir + infile_var, self.data_dir + "testOutfile"], [self.data_dir + infile_var, self.data_dir + "testOutfile.predict"]) self.assertEqual(extract.get_all_switches(), expected)