def test_GGAG_at_same_position(self):
library = ("AGGAGCCATCTTCTATCT",
"AGGAGAGAGTTATCCGAC")
motif = "GGAG"
expected = [0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
results = Sequences.motif_position_counts(library, motif)
self.assertEqual(expected, results)
def test_basic(self):
rc = Sequences.reverse_complement("GGAGG")
self.assertEqual(rc, "CCUCC")
def test_some_of_every_base(self):
usage = Sequences.get_base_usage("AGCUAGCU")
self.assertEqual(usage["A"], 2)
self.assertEqual(usage["C"], 2)
self.assertEqual(usage["G"], 2)
self.assertEqual(usage["U"], 2)
def test_nothing(self):
library = ("A"*18, "G"*18, "C"*18)
motif = "UUU"
results = Sequences.motif_position_counts(library, motif)
self.assertEqual([0]*18, results)
def setUp(self):
db = "/Users/barendt/git/fresh_start/data/sequences.sqlite"
self.sequences = Sequences.load_raw_records_from_db(db, 1, 1)
def test_cleaned_record_count(self):
db = "/Users/barendt/git/fresh_start/data/sequences.sqlite"
sequences = Sequences.load_from_db(db, 11, 2)
self.assertEqual(len(sequences), 5151)
def test_in_frame_aug(self):
self.assertTrue(Sequences.has_inframe_aug("AUGGCUAGUAAGGAUCU"))
def test_out_of_frame_aug(self):
self.assertFalse(Sequences.has_inframe_aug("AAUGGCUAGUAGGAUCU"))
def test_no_aug(self):
self.assertFalse(Sequences.has_inframe_aug("AGGUCCUAGUAGGAUCU"))
