def test_build_index(self):
# No annotation
return_code1 = star.build_index(self.genome,
self.index_dir,
overhang=100,
overhang_min=8,
threads=1)
# With annotation
return_code2 = star.build_index(self.genome,
self.index_dir,
annotation=self.annotation,
overhang=100,
overhang_min=8,
threads=1)
self.assertEqual(return_code1, 0)
self.assertEqual(return_code2, 0)
def test_map_reads(self):
# First: make index:
# Give logfile_path to some /tmp location to not pollute woking directory
star.build_index(self.genome, self.index_dir)
# No annotation
return_code1 = star.map_reads(self.reads, self.index_dir, self.dir)
# With annotation:
return_code2 = star.map_reads(self.reads,
self.index_dir,
self.dir,
annotation=self.annotation,
multimax=10,
mismatches=2,
threads=1)
self.assertEqual(return_code1, 0)
self.assertEqual(return_code2, 0)
def test_build_index_bad_outdir(self):
message = r'Output directory does not exist. Make sure it does.'
with self.assertRaisesRegex(FileNotFoundError, message):
star.build_index(self.genome, '/unexisting/outdir')