def eval_transcripts(self, data):
'''
For passed set of transcripts, evaluate using error
methods defined in Hah et al.
'''
evaluator = TranscriptEvaluator()
evaluator.set_reference(self.reference)
evaluator.set_target(data)
return evaluator.get_summed_error()
class TranscriptEvaluatorTest(unittest.TestCase):
evaluator = None
def setUp(self):
self.evaluator = TranscriptEvaluator()
ref = pandas.read_csv(StringIO(genes), sep=' ', header=None)
self.evaluator.set_reference(ref)
super(TranscriptEvaluatorTest, self).setUp()
def _get_count_broken(self, data_str):
target = pandas.read_csv(StringIO(data_str), sep=' ', header=None)
self.evaluator.set_target(target)
return self.evaluator.count_broken_reference()
def _get_count_run_together(self, data_str):
target = pandas.read_csv(StringIO(data_str), sep=' ', header=None)
self.evaluator.set_target(target)
return self.evaluator.count_run_together_reference()
def test_no_overlap(self):
'''
Neg control.
[-------------------]
[--------]
'''
data_str = 'chr1 800 900 +'
self.assertFalse(self._get_count_broken(data_str))
self.assertFalse(self._get_count_run_together(data_str))
def test_start_overlap(self):
'''
Neg control.
[-------------------]
[----------]
'''
data_str = 'chr1 50 150 +'
self.assertFalse(self._get_count_broken(data_str))
self.assertFalse(self._get_count_run_together(data_str))
def test_end_overlap(self):
'''
Neg control.
[-------------------]
[------------]
'''
data_str = 'chr1 150 250 +'
self.assertFalse(self._get_count_broken(data_str))
self.assertFalse(self._get_count_run_together(data_str))
def test_gene_containment(self):
'''
Neg control.
[-------------------]
[---------------------------]
'''
data_str = 'chr1 50 250 +'
self.assertFalse(self._get_count_broken(data_str))
self.assertFalse(self._get_count_run_together(data_str))
def test_target_containment(self):
'''
Neg control.
[-------------------]
[-------------]
'''
data_str = 'chr1 125 175 +'
self.assertFalse(self._get_count_broken(data_str))
self.assertFalse(self._get_count_run_together(data_str))
def test_diff_strand(self):
'''
Neg control.
[-------------------] +
[-------------] [-------------] -
'''
data_str = 'chr1 50 150 -'\
+ '\nchr1 175 250 -'
self.assertFalse(self._get_count_broken(data_str))
self.assertFalse(self._get_count_run_together(data_str))
def test_diff_chr(self):
'''
Neg control.
[-------------------] 1
[-------------] [-------------] 2
'''
data_str = 'chr2 50 150 +'\
+ '\nchr2 175 250 +'
self.assertFalse(self._get_count_broken(data_str))
self.assertFalse(self._get_count_run_together(data_str))
def test_broken_overlap(self):
'''
Pos control.
[-------------------]
[-------------] [-------------]
'''
data_str = 'chr1 50 150 +'\
+ '\nchr1 175 250 +'
self.assertEqual(self._get_count_broken(data_str), 1)
self.assertFalse(self._get_count_run_together(data_str))
def test_broken_contained(self):
'''
Pos control.
[-------------------]
[------] [------]
'''
data_str = 'chr1 100 125 +'\
+ '\nchr1 150 175 +'
self.assertEqual(self._get_count_broken(data_str), 1)
self.assertFalse(self._get_count_run_together(data_str))
def test_many_broken(self):
'''
Pos control.
[-------------------]
[-------] [----] [-------------]
'''
data_str = 'chr1 50 125 +'\
+ '\nchr1 130 150 +'\
+ '\nchr1 175 250 +'
self.assertEqual(self._get_count_broken(data_str), 1)
self.assertFalse(self._get_count_run_together(data_str))
def test_broken_boundary(self):
'''
Pos control.
[-------------------]
[---] [------]
'''
data_str = 'chr1 50 100 +'\
+ '\nchr1 200 250 +'
self.assertEqual(self._get_count_broken(data_str), 1)
self.assertFalse(self._get_count_run_together(data_str))
def test_run_together_overlap(self):
'''
Pos control.
[--------] [--------]
[-------------------------]
'''
data_str = 'chr1 150 350 +'
self.assertFalse(self._get_count_broken(data_str))
self.assertEqual(self._get_count_run_together(data_str), 1)
def test_run_together_contained(self):
'''
Pos control.
[--------] [--------]
[-------------------------------]
'''
data_str = 'chr1 50 550 +'
self.assertFalse(self._get_count_broken(data_str))
self.assertEqual(self._get_count_run_together(data_str), 1)
def test_broken_isoforms(self):
'''
Pos control.
[---------------]
[-------------------]
[-------------] [-------------]
'''
data_str = 'chr1 550 650 -'\
+ '\nchr1 675 850 -'
self.assertEqual(self._get_count_broken(data_str), 2)
self.assertFalse(self._get_count_run_together(data_str))