def setUp(self):
ft_gene = Feature_Type(type='Gene')
ft_gene.save()
self.dna = 'ATTGCGGATCGCGAATGCGATCG'
self.pro = 'MKKKAPSI'
self.pro_dna = 'ATGAAGAAGAAAGCACCAAGCATA'
self.feature1 = Feature(type=ft_gene, name='G1', sequence=self.dna)
self.feature1.as_dna()
self.feature1.save()
self.feature2 = Feature(type=ft_gene, name='G2', sequence=self.pro)
self.feature2.as_protein()
self.feature2.save()
self.feature_db = Feature_Database(name='test')
self.feature_db.save()
self.feature_db.features.add(self.feature1, self.feature2)
class BlastTest(TestCase):
def setUp(self):
ft_gene = Feature_Type(type='Gene')
ft_gene.save()
self.dna = 'ATTGCGGATCGCGAATGCGATCG'
self.pro = 'MKKKAPSI'
self.pro_dna = 'ATGAAGAAGAAAGCACCAAGCATA'
self.feature1 = Feature(type=ft_gene, name='G1', sequence=self.dna)
self.feature1.as_dna()
self.feature1.save()
self.feature2 = Feature(type=ft_gene, name='G2', sequence=self.pro)
self.feature2.as_protein()
self.feature2.save()
self.feature_db = Feature_Database(name='test')
self.feature_db.save()
self.feature_db.features.add(self.feature1, self.feature2)
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))
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_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_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_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))
class IntegrationTest(TestCase):
def setUp(self):
ft_gene = Feature_Type(type='Gene')
ft_gene.save()
self.dna = 'ATTGCGGATCGCGAATGCGATCG'
self.pro = 'MKKKAPSI'
self.pro_dna = 'ATGAAGAAGAAAGCACCAAGCATA'
self.feature1 = Feature(type=ft_gene, name='G1', sequence=self.dna)
self.feature1.as_dna()
self.feature1.save()
self.feature2 = Feature(type=ft_gene, name='G2', sequence=self.pro)
self.feature2.as_protein()
self.feature2.save()
self.feature_db = Feature_Database(name='test')
self.feature_db.save()
self.feature_db.features.add(self.feature1, self.feature2)
def test_build_db(self):
self.feature_db.build()
def test_finds_orf_in_both_directions_and_across_boundary(self):
self.feature_db.build()
query = 'G'*100+'ATG'+'C'*3000+'TAG'+'CTA'+'G'*1800+'CAT'
data = {'db': self.feature_db.name, 'sequence': query}
url = reverse('giraffe-analyze')
resp = self.client.post(url, data)
self.assertEquals(resp.status_code, 200)
res = json.loads(resp.content)
self.assertEquals(res[0], len(query))
self.assertItemsEqual(res[1],
[
{'orf_frame': 1,
'layer': 'ORFs',
'type_id': 10,
'subject_start': 1,
'subject_end': 3+3000+3,
'query_start': 100+1,
'query_end': 100+3+3000+3,
'label': 'ORF frame 2',
'name': 'ORF frame 2'},
{'orf_frame': 0,
'layer': 'ORFs',
'type_id': 10,
'subject_start': 3+1800+3,
'subject_end': 1,
'query_start': 100+3+3000+3+1,
'query_end': 100+3+3000+3+3+1800+3,
'label': 'ORF frame 1',
'name': 'ORF frame 1'},
# across circular boundary, there is AT, then G, it ends with the first
# stop codon after C*3000
{'orf_frame': 2,
'layer': 'ORFs',
'type_id': 10,
'subject_start': 1,
'subject_end': 3+99+3+3000+3,
'query_start': len(query)-2+1,
'query_end': 100+3+3000+3,
'label': 'ORF frame 3',
'name': 'ORF frame 3'}
]
)
def test_does_not_find_orf_across_boundary_if_not_in_circular_mode(self):
self.feature_db.build()
query = 'G'*100+'ATG'+'C'*3000+'TAG'+'CTA'+'G'*1800+'CAT'
data = {'db': self.feature_db.name, 'sequence': query, 'circular': 0}
url = reverse('giraffe-analyze')
resp = self.client.post(url, data)
self.assertEquals(resp.status_code, 200)
res = json.loads(resp.content)
self.assertEquals(res[0], len(query))
self.assertItemsEqual(res[1],
[
{'orf_frame': 1,
'layer': 'ORFs',
'type_id': 10,
'subject_start': 1,
'subject_end': 3+3000+3,
'query_start': 100+1,
'query_end': 100+3+3000+3,
'label': 'ORF frame 2',
'name': 'ORF frame 2'},
{'orf_frame': 0,
'layer': 'ORFs',
'type_id': 10,
'subject_start': 3+1800+3,
'subject_end': 1,
'query_start': 100+3+3000+3+1,
'query_end': 100+3+3000+3+3+1800+3,
'label': 'ORF frame 1',
'name': 'ORF frame 1'}
]
)
def test_find_tags_within_orf(self):
self.feature_db.build()
query = 'G'*100+'ATG'+'C'*3000+'CAT'*6+'TAG'
data = {'db': self.feature_db.name, 'sequence': query, 'circular': 0}
url = reverse('giraffe-analyze')
resp = self.client.post(url, data)
self.assertEquals(resp.status_code, 200)
res = json.loads(resp.content)
self.assertEquals(res[0], len(query))
self.assertItemsEqual(res[1],
[
{'orf_frame': 1,
'layer': 'ORFs',
'type_id': 10,
'subject_start': 1,
'subject_end': 3+3000+3*6+3,
'query_start': 100+1,
'query_end': 100+3+3000+3*6+3,
'label': 'ORF frame 2',
'name': 'ORF frame 2'},
{'layer': 'Detected Features',
'type_id': 1,
'subject_start': 1,
'subject_end': 3*6,
'query_start': 100+3+3000+1,
'query_end': 100+3+3000+3*6,
'label': '6xHIS',
'name': '6xHIS'}
]
)
def test_blastn(self):
self.feature_db.build()
data = {'db': self.feature_db.name, 'sequence': self.dna}
url = reverse('giraffe-analyze')
resp = self.client.post(url, data)
self.assertEquals(resp.status_code, 200)
res = json.loads(resp.content)
self.assertEquals(res[0], len(self.dna))
self.assertItemsEqual(res[1],
[{"layer": "Detected Features",
"name": "G1",
"type_id": 5,
"label": "G1",
"query_start": 1,
"query_end": 23,
"subject_start": 1,
"subject_end": 23,
"evalue": 6.01355e-11,
"identities": 23,
"alignment": { "query": "ATTGCGGATCGCGAATGCGATCG",
"match": "|||||||||||||||||||||||",
"subject": "ATTGCGGATCGCGAATGCGATCG"}},
{"layer": "Restriction Enzymes",
"name": "NruI", "type_id": 4, "elucidate": "TCG^_CGA", "label": "NruI",
"query_start": 9, "cut": 11, "query_end": 14, "subject_start": 1, "subject_end": 6},
{"layer": "Restriction Enzymes",
"name": "ClaI", "type_id": 4, "elucidate": "AT^CG_AT", "label": "ClaI",
"query_start": 20, "cut": 21, "query_end": 2, "subject_start": 1, "subject_end": 6},
]
)
def test_blastx(self):
self.feature_db.build()
q = 'A'+self.pro_dna+'T'
data = {'db': self.feature_db.name, 'sequence': q}
url = reverse('giraffe-analyze')
resp = self.client.post(url, data)
self.assertEquals(resp.status_code, 200)
res = json.loads(resp.content)
self.assertEquals(res[0], len(q))
self.assertItemsEqual(res[1], [
{"layer": "Detected Features",
"query_start": 2,
"query_end": 25,
"subject_start" : 1,
"subject_end" : 8,
"name": "G2",
"type_id": 5,
"label": "G2",
"alignment": {"query": "MKKKAPSI", "match": "MKKKAPSI", "subject": "MKKKAPSI"},
"evalue": 5.42133e-5,
"identities": 8
}
])
def test_blast2(self):
data = {'subject': self.dna, 'query': self.dna[0:22]+'T'}
url = reverse('blast2')
resp = self.client.post(url, data)
self.assertEquals(resp.status_code, 200)
res = json.loads(resp.content)
self.assertItemsEqual(res, [
{ "subject_start": 1, "subject_end": 22,
"query_start": 1, "query_end": 22,
"evalue": 5.81644e-07,
"query": "ATTGCGGATCGCGAATGCGATC",
"match": "||||||||||||||||||||||",
"subject": "ATTGCGGATCGCGAATGCGATC" },
])
