def test_blast_evalue_threshold(self):
self.feature_db.build()
query = 'G'*100+self.dna+'A'*40
feature_list = blast(query, self.feature_db)
self.assertEquals(len(feature_list), 1)
feature_list = blast(query, self.feature_db, evalue_threshold=1E-50)
self.assertEquals(len(feature_list), 0)
def test_blast_feature_threshold(self):
self.feature_db.build()
p = 0.8
n = int(len(self.dna)*p)
query = 'G'*100+self.dna[0:n]+'A'*40
feature_list = blast(query, self.feature_db, feature_threshold=None)
self.assertEquals(len(feature_list), 1)
self.assertEquals(feature_list[0].query_start, 101)
self.assertEquals(feature_list[0].query_end, 100+n)
self.assertEquals(feature_list[0].subject_start, 1)
self.assertEquals(feature_list[0].subject_end, n)
feature_list = blast(query, self.feature_db, feature_threshold=p)
self.assertEquals(len(feature_list), 0)
def test_get_feature_from_blast_result(self):
self.feature_db.build()
query = 'G'*100+self.dna+'A'*40
feature_list = blast(query, self.feature_db)
self.assertEquals(len(feature_list), 1)
self.assertEquals(feature_list[0].feature_id, self.feature1.id)
def test_returns_one_result_from_across_circular_boundary(self): self.feature_db.build() q = 'G'*100+self.dna+'A'*40 query = q[110:]+q[0:110] feature_list = blast(query, self.feature_db) # if we don't remove truncated features across circular boundary, we'd see # 2 results, one for truncated feature, one for full feature self.assertEquals(len(feature_list), 1)
def test_blast_identity_threshold(self):
self.feature_db.build()
q = self.dna
# make two changes
q = q[0:3]+'C'+q[4:6]+'C'+q[7:]
self.assertEquals(len(q), len(self.dna))
query = 'G'*100+q+'A'*40
feature_list = blast(query, self.feature_db, identity_threshold=None)
self.assertEquals(len(feature_list), 1)
self.assertEquals(feature_list[0].query_start, 101)
self.assertEquals(feature_list[0].query_end, 100+len(self.dna))
self.assertEquals(feature_list[0].subject_start, 1)
self.assertEquals(feature_list[0].subject_end, len(self.dna))
feature_list = blast(query, self.feature_db, identity_threshold=0.99)
self.assertEquals(len(feature_list), 0)
def test_returns_correct_coordinates_across_circular_boundary(self):
self.feature_db.build()
q = 'G'*100+self.dna+'A'*40
query = q[110:]+q[0:110]
feature_list = blast(query, self.feature_db)
self.assertEquals(feature_list[0].query_start, len(q)-10+1)
self.assertEquals(feature_list[0].query_end, len(self.dna)-10)
self.assertEquals(feature_list[0].subject_start, 1)
self.assertEquals(feature_list[0].subject_end, len(self.dna))
def test_blast(self):
self.feature_db.build()
query = 'G'*100+self.dna+'A'*40
feature_list = blast(query, self.feature_db)
self.assertEquals(len(feature_list), 1)
self.assertEquals(feature_list[0].name, self.feature1.name)
self.assertEquals(feature_list[0].query_start, 101)
self.assertEquals(feature_list[0].query_end, 100+len(self.dna))
self.assertEquals(feature_list[0].subject_start, 1)
self.assertEquals(feature_list[0].subject_end, len(self.dna))