def test_add_analyses_option(self):
cli = CLI("Test")
cli.add_analyses_option()
options,args = cli.parse_args(list())
self.assertEqual(options.analyses,'all')
options,args = cli.parse_args(['--analyses=all',])
self.assertEqual(options.analyses,'all')
options,args = cli.parse_args(['--analyses=peak_centric',])
self.assertEqual(options.analyses,'peak_centric')
options,args = cli.parse_args(['--analyses=gene_centric',])
self.assertEqual(options.analyses,'gene_centric')
def test_add_edge_option(self):
cli = CLI("Test")
cli.add_edge_option()
options,args = cli.parse_args(list())
self.assertEqual(options.edge,'tss')
options,args = cli.parse_args(['--edge=tss',])
self.assertEqual(options.edge,'tss')
options,args = cli.parse_args(['--edge=both',])
self.assertEqual(options.edge,'both')
def test_add_option_group(self):
cli = CLI("Test")
cli.add_option_group("Example options")
cli.add_option('--attempts',
dest='attempts',
default=0,
type=int,
help="Number of attempts",
group="Example options")
options,args = cli.parse_args(list())
self.assertEqual(options.attempts,0)
options,args = cli.parse_args(['--attempts=11',])
self.assertEqual(options.attempts,11)
def test_add_summary_option(self):
cli = CLI("Test")
cli.add_summary_option()
options,args = cli.parse_args(list())
self.assertFalse(options.summary)
options,args = cli.parse_args(['--summary',])
self.assertTrue(options.summary)
def test_add_compact_option(self):
cli = CLI("Test")
cli.add_compact_option()
options,args = cli.parse_args(list())
self.assertFalse(options.compact)
options,args = cli.parse_args(['--compact',])
self.assertTrue(options.compact)
def test_name_option(self):
cli = CLI("Test")
cli.add_name_option()
options,args = cli.parse_args(list())
self.assertEqual(options.name,None)
options,args = cli.parse_args(['--name=test',])
self.assertEqual(options.name,"test")
def test_add_promoter_region_option(self):
cli = CLI("Test")
cli.add_promoter_region_option()
options,args = cli.parse_args(list())
self.assertEqual(options.promoter_region,"1000,100")
options,args = cli.parse_args(['--promoter_region=1500,200',])
self.assertEqual(options.promoter_region,"1500,200")
def test_add_number_option(self):
cli = CLI("Test")
cli.add_number_option()
options,args = cli.parse_args(list())
self.assertEqual(options.max_closest,None)
options,args = cli.parse_args(['--number=9',])
self.assertEqual(options.max_closest,9)
def test_add_only_de_option(self):
cli = CLI("Test")
cli.add_only_de_option()
options,args = cli.parse_args(list())
self.assertFalse(options.only_diff_expressed)
options,args = cli.parse_args(['--only-DE',])
self.assertTrue(options.only_diff_expressed)
def test_add_peak_cols_option(self):
cli = CLI("Test")
cli.add_peak_cols_option()
options,args = cli.parse_args(list())
self.assertEqual(options.peak_cols,None)
options,args = cli.parse_args(['--peak_cols=3,1,2',])
self.assertEqual(options.peak_cols,"3,1,2")
def test_peak_id_option(self):
cli = CLI("Test")
cli.add_peak_id_option()
options,args = cli.parse_args(list())
self.assertEqual(options.peak_id,None)
options,args = cli.parse_args(['--peak_id=4',])
self.assertEqual(options.peak_id,4)
def test_feature_option(self):
cli = CLI("Test")
cli.add_feature_option()
options,args = cli.parse_args(list())
self.assertEqual(options.feature_type,'gene')
options,args = cli.parse_args(['--feature=transcript',])
self.assertEqual(options.feature_type,"transcript")
def test_add_xlsx_option(self):
cli = CLI("Test")
cli.add_xlsx_option()
options,args = cli.parse_args(list())
self.assertFalse(options.xlsx_output)
options,args = cli.parse_args(['--xlsx',])
self.assertTrue(options.xlsx_output)
def test_get_version(self):
cli = CLI("Test",version="v1.0.2")
self.assertEqual(cli.get_version(),"v1.0.2")