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)
