def test_kmc_in_path(self):
'''Test kmc in path'''
self.assertTrue(
external_progs.is_in_path('kmc'),
'Error! Did not find kmc in your path! Please install kmc')
def test_samtools_in_path(self):
'''Test samtools in path'''
self.assertTrue(
external_progs.is_in_path('samtools'),
'Error! Did not find samtools in your path! Please install samtools'
)
def test_smalt_in_path(self):
'''Test smalt in path'''
self.assertTrue(
external_progs.is_in_path('smalt'),
'Error! Did not find smalt in your path! Please install smalt')
def test_delta_filter_in_path(self):
'''Test delta-filter in path'''
self.assertTrue(
external_progs.is_in_path('delta-filter'),
'Error! Did not find delta-filter in your path! Please install MUMmer'
)
def test_show_coords_in_path(self):
'''Test show-coords in path'''
self.assertTrue(
external_progs.is_in_path('show-coords'),
'Error! Did not find show-coords in your path! Please install MUMmer'
)
def test_kmc_dump_in_path(self):
'''Test kmc_dump in path'''
self.assertTrue(external_progs.is_in_path('kmc_dump'), 'Error! Did not find kmc_dump in your path! Please install kmc')
def test_nucmer_in_path(self):
'''Test nucmer in path'''
self.assertTrue(
external_progs.is_in_path('nucmer'),
'Error! Did not find nucmer in your path! Please install MUMmer')
def test_smalt_in_path(self):
'''Test smalt in path'''
self.assertTrue(external_progs.is_in_path('smalt'), 'Error! Did not find smalt in your path! Please install smalt')
def test_samtools_in_path(self):
'''Test samtools in path'''
self.assertTrue(external_progs.is_in_path('samtools'), 'Error! Did not find samtools in your path! Please install samtools')
def test_show_coords_in_path(self):
'''Test show-coords in path'''
self.assertTrue(external_progs.is_in_path('show-coords'), 'Error! Did not find show-coords in your path! Please install MUMmer')
def test_delta_filter_in_path(self):
'''Test delta-filter in path'''
self.assertTrue(external_progs.is_in_path('delta-filter'), 'Error! Did not find delta-filter in your path! Please install MUMmer')
def test_nucmer_in_path(self):
'''Test nucmer in path'''
self.assertTrue(external_progs.is_in_path('nucmer'), 'Error! Did not find nucmer in your path! Please install MUMmer')
