def test_blast_aligns_sequence_to_antisense_strand(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
query = str(Seq(s1[6:20]).reverse_complement()) + 'tttttttttt'
res = self.client.post('/edge/genomes/%s/blast/' % g1.id,
data=json.dumps(
dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f1.id)
self.assertEquals(d[0]['query_start'], 1)
self.assertEquals(d[0]['query_end'], 14)
self.assertEquals(d[0]['subject_start'], 20)
self.assertEquals(d[0]['subject_end'], 7)
def test_finds_genomes_with_name(self):
from edge.models import Genome
a = Genome(name="Foo")
a.save()
Genome(name="Bar %s" % a.id).save()
# no filter, return both genomes
url = reverse("genome_list")
res = self.client.get(url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["name"] for g in d], ["Foo", "Bar %s" % a.id])
# finds genome by ID and query
res = self.client.get("%s?q=%s" % (url, a.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["name"] for g in d], ["Foo", "Bar %s" % a.id])
# finds one
res = self.client.get("%s?q=oo" % url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["name"] for g in d], ["Foo"])
# finds none
res = self.client.get("%s?q=ooo" % url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["name"] for g in d], [])
def test_finds_sequence_on_specified_genome(self):
s1 = get_random_sequence(200)
s2 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
f2 = Fragment.create_with_sequence("Baz", s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name="Far")
g2.save()
f3 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[6:20] + "aaaaaaaaa"
r = blast_genome(g1, "blastn", query)
# only returns hit from genome
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 7)
self.assertEquals(r[0].subject_end, 20)
self.assertEquals(r[0].strand(), 1)
def test_blast_aligns_sequence_to_antisense_strand(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
query = str(Seq(s1[6:20]).reverse_complement()) + "tttttttttt"
res = self.client.post(
"/edge/genomes/%s/blast/" % g1.id,
data=json.dumps(dict(program="blastn", query=query)),
content_type="application/json",
)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(len(d), 1)
self.assertEquals(d[0]["fragment_id"], f1.id)
self.assertEquals(d[0]["query_start"], 1)
self.assertEquals(d[0]["query_end"], 14)
self.assertEquals(d[0]["subject_start"], 20)
self.assertEquals(d[0]["subject_end"], 7)
def test_finds_sequence_on_specified_genome(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
s2 = 'agcgtcgatgcatgagtcgatcggcagtcgtgtagtcgtcgtatgcgtta'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
f2 = Fragment.create_with_sequence('Baz', s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name='Far')
g2.save()
f3 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[6:20] + 'aaaaaaaaa'
r = blast_genome(g1, 'blastn', query)
# only returns hit from genome
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 7)
self.assertEquals(r[0].subject_end, 20)
self.assertEquals(r[0].strand(), 1)
def test_finds_sequence_on_specified_genome(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
s2 = 'agcgtcgatgcatgagtcgatcggcagtcgtgtagtcgtcgtatgcgtta'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
f2 = Fragment.create_with_sequence('Baz', s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name='Far')
g2.save()
f3 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[6:20] + 'aaaaaaaaa'
r = blast_genome(g1, 'blastn', query)
# only returns hit from genome
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 7)
self.assertEquals(r[0].subject_end, 20)
self.assertEquals(r[0].strand(), 1)
def test_finds_genomes_with_name(self):
from edge.models import Genome
a = Genome(name='Foo')
a.save()
Genome(name='Bar %s' % a.id).save()
# no filter, return both genomes
res = self.client.get('/edge/genomes/')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])
# finds genome by ID and query
res = self.client.get('/edge/genomes/?q=%s' % a.id)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])
# finds one
res = self.client.get('/edge/genomes/?q=oo')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo'])
# finds none
res = self.client.get('/edge/genomes/?q=ooo')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], [])
def test_blast_aligns_sequence_to_antisense_strand(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
query = str(Seq(s1[6:20]).reverse_complement())+'tttttttttt'
res = self.client.post('/edge/genomes/%s/blast/' % g1.id,
data=json.dumps(dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
# only returns hit from genome
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f1.id)
self.assertEquals(d[0]['query_start'], 1)
self.assertEquals(d[0]['query_end'], 14)
self.assertEquals(d[0]['subject_start'], 20)
self.assertEquals(d[0]['subject_end'], 7)
def test_finds_genomes_with_name(self):
from edge.models import Genome
a = Genome(name='Foo')
a.save()
Genome(name='Bar %s' % a.id).save()
# no filter, return both genomes
res = self.client.get('/edge/genomes/')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])
# finds genome by ID and query
res = self.client.get('/edge/genomes/?q=%s' % a.id)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])
# finds one
res = self.client.get('/edge/genomes/?q=oo')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo'])
# finds none
res = self.client.get('/edge/genomes/?q=ooo')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], [])
def test_finds_genomes_with_specified_fragment_ids(self):
g1 = Genome(name="Foo")
g1.save()
g2 = Genome(name="Bar")
g2.save()
f1 = Fragment(circular=True, name="FooF1")
f1.save()
f2 = Fragment(circular=True, name="FooF2")
f2.save()
f3 = Fragment(circular=True, name="FooF3", parent=f2)
f3.save()
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
Genome_Fragment(genome=g2, fragment=f1, inherited=True).save()
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
# no filter, return both genomes
url = reverse("genome_list")
res = self.client.get(url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["id"] for g in d], [g1.id, g2.id])
# looking for f1 and f2
res = self.client.get("%s?f=%d&f=%d" % (url, f1.id, f2.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["id"] for g in d], [g1.id])
# looking for f1 and f3
res = self.client.get("%s?f=%d&f=%d" % (url, f1.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["id"] for g in d], [g2.id])
# looking for f2 and f3
res = self.client.get("%s?f=%d&f=%d" % (url, f2.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# looking for f1
res = self.client.get("%s?f=%d" % (
url,
f1.id,
))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# bad input, return []
res = self.client.get("%s?f=[1,2,3]" % url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
def build_genome_and_ancestors(self, names):
# build a genome of name in names with each as its subsquent genome's parent
g_parent = Genome(name=names[0])
g_parent.save()
g_child = g_parent
for name in names[:-1]:
g_child = Genome(name=name)
g_child.parent = g_parent
g_child.save()
g_parent = g_child
return g_child
def test_finds_genomes_with_specified_fragment_ids(self):
from edge.models import Genome, Fragment, Genome_Fragment
g1 = Genome(name='Foo')
g1.save()
g2 = Genome(name='Bar')
g2.save()
f1 = Fragment(circular=True, name='FooF1')
f1.save()
f2 = Fragment(circular=True, name='FooF2')
f2.save()
f3 = Fragment(circular=True, name='FooF3', parent=f2)
f3.save()
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
Genome_Fragment(genome=g2, fragment=f1, inherited=True).save()
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
# no filter, return both genomes
res = self.client.get('/edge/genomes/')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['id'] for g in d], [g1.id, g2.id])
# looking for f1 and f2
res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f1.id, f2.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['id'] for g in d], [g1.id])
# looking for f1 and f3
res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f1.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['id'] for g in d], [g2.id])
# looking for f2 and f3
res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f2.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# looking for f1
res = self.client.get('/edge/genomes/?f=%d' % (f1.id,))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# bad input, return []
res = self.client.get('/edge/genomes/?f=[1,2,3]')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
def build_genome(self, circular, *templates):
g = Genome(name='Foo')
g.save()
for seq in templates:
f = Fragment.create_with_sequence('Bar', seq, circular=circular)
Genome_Fragment(genome=g, fragment=f, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f))
except:
pass
build_all_genome_dbs(refresh=True)
return Genome.objects.get(pk=g.id)
def test_blast_finds_sequence_on_specified_genome(self):
s1 = get_random_sequence(200)
s2 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
f2 = Fragment.create_with_sequence("Baz", s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name="Far")
g2.save()
f3 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
query = s1[6:20] + "aaaaaaaaa"
res = self.client.post(
"/edge/genomes/%s/blast/" % g1.id,
data=json.dumps(dict(program="blastn", query=query)),
content_type="application/json",
)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
# only returns hit from genome
self.assertEquals(len(d), 1)
self.assertEquals(d[0]["fragment_id"], f1.id)
self.assertEquals(d[0]["query_start"], 1)
self.assertEquals(d[0]["query_end"], 14)
self.assertEquals(d[0]["subject_start"], 7)
self.assertEquals(d[0]["subject_end"], 20)
# blast in other genome works too
res = self.client.post(
"/edge/genomes/%s/blast/" % g2.id,
data=json.dumps(dict(program="blastn", query=query)),
content_type="application/json",
)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(len(d), 1)
self.assertEquals(d[0]["fragment_id"], f3.id)
def test_finds_genomes_with_specified_fragment_ids(self):
g1 = Genome(name='Foo')
g1.save()
g2 = Genome(name='Bar')
g2.save()
f1 = Fragment(circular=True, name='FooF1')
f1.save()
f2 = Fragment(circular=True, name='FooF2')
f2.save()
f3 = Fragment(circular=True, name='FooF3', parent=f2)
f3.save()
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
Genome_Fragment(genome=g2, fragment=f1, inherited=True).save()
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
# no filter, return both genomes
res = self.client.get('/edge/genomes/')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['id'] for g in d], [g1.id, g2.id])
# looking for f1 and f2
res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f1.id, f2.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['id'] for g in d], [g1.id])
# looking for f1 and f3
res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f1.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['id'] for g in d], [g2.id])
# looking for f2 and f3
res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f2.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# looking for f1
res = self.client.get('/edge/genomes/?f=%d' % (f1.id, ))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# bad input, return []
res = self.client.get('/edge/genomes/?f=[1,2,3]')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
def test_builds_genome_db_with_different_names_on_separate_attempts(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
dbname1 = build_genome_db(g1)
self.assertEquals(dbname1 is None, False)
self.assertEquals(dbname1, g1.blastdb)
g1.blastdb = None
dbname2 = build_genome_db(g1)
self.assertEquals(dbname2 == dbname1, False)
def test_does_not_return_genomic_fragments(self):
from edge.models import Genome, Genome_Fragment
res = self.client.get('/edge/fragments/')
self.assertEquals(res.status_code, 200)
self.assertEquals(len(json.loads(res.content)), 1)
g = Genome(name='Foo')
g.save()
Genome_Fragment(genome=g, fragment_id=self.fragment_id, inherited=False).save()
res = self.client.get('/edge/fragments/')
self.assertEquals(res.status_code, 200)
self.assertEquals(len(json.loads(res.content)), 0)
def test_blast_finds_sequence_on_specified_genome(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
s2 = 'agcgtcgatgcatgagtcgatcggcagtcgtgtagtcgtcgtatgcgtta'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
f2 = Fragment.create_with_sequence('Baz', s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name='Far')
g2.save()
f3 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except:
pass
build_all_genome_dbs(refresh=True)
query = s1[6:20] + 'aaaaaaaaa'
res = self.client.post('/edge/genomes/%s/blast/' % g1.id,
data=json.dumps(
dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
# only returns hit from genome
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f1.id)
self.assertEquals(d[0]['query_start'], 1)
self.assertEquals(d[0]['query_end'], 14)
self.assertEquals(d[0]['subject_start'], 7)
self.assertEquals(d[0]['subject_end'], 20)
# blast in other genome works too
res = self.client.post('/edge/genomes/%s/blast/' % g2.id,
data=json.dumps(
dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f3.id)
def test_does_not_return_genomic_fragments(self):
from edge.models import Genome, Genome_Fragment
res = self.client.get('/edge/fragments/')
self.assertEquals(res.status_code, 200)
self.assertEquals(len(json.loads(res.content)), 1)
g = Genome(name='Foo')
g.save()
Genome_Fragment(genome=g,
fragment_id=self.fragment_id,
inherited=False).save()
res = self.client.get('/edge/fragments/')
self.assertEquals(res.status_code, 200)
self.assertEquals(len(json.loads(res.content)), 0)
def test_blast_finds_sequence_on_specified_genome(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
s2 = 'agcgtcgatgcatgagtcgatcggcagtcgtgtagtcgtcgtatgcgtta'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
f2 = Fragment.create_with_sequence('Baz', s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name='Far')
g2.save()
f3 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except:
pass
build_all_genome_dbs(refresh=True)
query = s1[6:20]+'aaaaaaaaa'
res = self.client.post('/edge/genomes/%s/blast/' % g1.id,
data=json.dumps(dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
# only returns hit from genome
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f1.id)
self.assertEquals(d[0]['query_start'], 1)
self.assertEquals(d[0]['query_end'], 14)
self.assertEquals(d[0]['subject_start'], 7)
self.assertEquals(d[0]['subject_end'], 20)
# blast in other genome works too
res = self.client.post('/edge/genomes/%s/blast/' % g2.id,
data=json.dumps(dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f3.id)
def test_builds_fragment_fastas(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
fn = fragment_fasta_fn(f1)
try:
os.unlink(fn)
except BaseException:
pass
fn = build_fragment_fasta(f1)
records = list(SeqIO.parse(fn, "fasta"))
self.assertEquals(len(records), 1)
self.assertEquals(str(records[0].seq), s1)
def test_does_not_return_duplicate_hits_for_circular_fragments(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1, circular=True)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[5:20] + 'tttttttttt'
r = blast_genome(g1, 'blastn', query)
self.assertEquals(len(r), 1)
def test_does_not_return_duplicate_hits_for_circular_fragments(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1, circular=True)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[5:20] + 'tttttttttt'
r = blast_genome(g1, 'blastn', query)
self.assertEquals(len(r), 1)
def test_does_not_return_duplicate_hits_for_circular_fragments(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1, circular=True)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[5:20] + "tttttttttt"
r = blast_genome(g1, "blastn", query)
self.assertEquals(len(r), 1)
def test_derives_new_genome_with_multiple_fragments(self):
g1 = Genome(name="Foo")
g1.save()
url = reverse("derive-genome-with-new-fragments",
kwargs={"genome_id": g1.id})
res = self.client.post(
url,
data=json.dumps([
{
"name": "test-fragment",
"sequence": "AGCTAGCTTCGATCGA"
},
{
"name": "circular-fragment",
"sequence": "AGCTAGCTTCGATCGAAGCTATTATATCGATA",
"circular": True,
},
]),
content_type="application/json",
)
self.assertEquals(res.status_code, 201)
child = Genome.objects.get(parent=g1.id)
self.assertNotEquals(child.id, g1.id)
fragments = [{
"id": fragment.id,
"uri": "/edge/fragments/{}/".format(fragment.id),
"name": fragment.name,
"circular": fragment.circular,
"parent_id": None,
"length": fragment.indexed_fragment().length,
} for fragment in child.fragments.all()]
self.assertEquals(
json.loads(res.content),
{
"fragments": fragments,
"id": child.id,
"name": child.name,
"notes": None,
"parent_id": g1.id,
"parent_name": g1.name,
"uri": "/edge/genomes/{}/".format(child.id),
},
)
def test_derives_new_genome_after_adding_fragment(self):
g1 = Genome(name="Foo")
g1.save()
url = reverse("derive-genome-with-new-fragments",
kwargs={"genome_id": g1.id})
res = self.client.post(
url,
data=json.dumps([{
"name": "test-fragment",
"sequence": "AGCTAGCTTCGATCGA"
}]),
content_type="application/json",
)
self.assertEquals(res.status_code, 201)
child = Genome.objects.get(parent=g1.id)
self.assertNotEquals(child.id, g1.id)
fragment = child.fragments.first()
self.assertEquals(
json.loads(res.content),
{
"fragments": [{
"id": fragment.id,
"uri": "/edge/fragments/{}/".format(fragment.id),
"name": fragment.name,
"circular": fragment.circular,
"parent_id": None,
"length": 16,
}],
"id":
child.id,
"name":
child.name,
"notes":
None,
"parent_id":
g1.id,
"parent_name":
g1.name,
"uri":
"/edge/genomes/{}/".format(child.id),
},
)
def test_does_not_align_sequence_across_boundry_for_non_circular_fragment(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1, circular=False)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = (s1[-10:] + s1[0:10]) + 'tttttttttt'
res = blast_genome(g1, 'blastn', query)
for r in res:
self.assertEquals(r.subject_start > 0 and r.subject_start <= len(s1), True)
self.assertEquals(r.subject_end > 0 and r.subject_end <= len(s1), True)
def test_does_not_align_sequence_across_boundry_for_non_circular_fragment(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1, circular=False)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = (s1[-10:] + s1[0:10]) + "tttttttttt"
res = blast_genome(g1, "blastn", query)
for r in res:
self.assertEquals(r.subject_start > 0 and r.subject_start <= len(s1), True)
self.assertEquals(r.subject_end > 0 and r.subject_end <= len(s1), True)
def test_does_not_align_sequence_across_boundry_for_non_circular_fragment(
self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1, circular=False)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = (s1[-10:] + s1[0:10]) + 'tttttttttt'
res = blast_genome(g1, 'blastn', query)
for r in res:
self.assertEquals(
r.subject_start > 0 and r.subject_start <= len(s1), True)
self.assertEquals(r.subject_end > 0 and r.subject_end <= len(s1),
True)
def test_aligns_sequence_to_antisense_strand(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = str(Seq(s1[6:20]).reverse_complement()) + 'tttttttttt'
r = blast_genome(g1, 'blastn', query)
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 20)
self.assertEquals(r[0].subject_end, 7)
self.assertEquals(r[0].strand(), -1)
def test_aligns_sequence_to_antisense_strand(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = str(Seq(s1[6:20]).reverse_complement()) + 'tttttttttt'
r = blast_genome(g1, 'blastn', query)
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 20)
self.assertEquals(r[0].subject_end, 7)
self.assertEquals(r[0].strand(), -1)
def test_aligns_sequence_to_antisense_strand(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = str(Seq(s1[6:20]).reverse_complement()) + "tttttttttt"
r = blast_genome(g1, "blastn", query)
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 20)
self.assertEquals(r[0].subject_end, 7)
self.assertEquals(r[0].strand(), -1)
def test_aligns_sequence_across_boundry_for_circular_fragment(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1, circular=True)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = (s1[-10:] + s1[0:10]) + "ttttttttttt"
res = blast_genome(g1, "blastn", query)
# we are not removing redundant matches when matching across circular
# boundaries, since blasting across circular boundary of a genome is a
# rare case. so in this particular case, you will find two results, one
# for the end of the query at the start of the genome, one for across
# the circular boundary.
found = False
for r in res:
if r.query_start == 1 and r.query_end == 20:
self.assertEquals(r.fragment_id, f1.id)
self.assertEquals(r.query_start, 1)
self.assertEquals(r.query_end, 20)
self.assertEquals(r.subject_start, len(s1) - 10 + 1)
self.assertEquals(r.subject_end, len(s1) + 10)
self.assertEquals(r.fragment_length, len(s1))
self.assertEquals(r.strand(), 1)
found = True
break
self.assertEquals(found, True)
def test_doesnt_derives_new_genome_on_invalid_fragment(self):
g1 = Genome(name="Foo")
g1.save()
url = reverse("derive-genome-with-new-fragments",
kwargs={"genome_id": g1.id})
with self.assertRaises(forms.ValidationError) as exception:
self.client.post(
url,
data=json.dumps([
{
"name": "valid-fragment",
"sequence": "AGCTAGCTTCGATCGA"
},
{
"name": "invalid-fragment",
},
]),
content_type="application/json",
)
self.assertIn("sequence", exception.exception.error_dict)
# Ensure that when an error is hit, no child genome was derived from the initially
# valid fragments
self.assertEqual(Genome.objects.filter(parent=g1.id).count(), 0)
def test_aligns_sequence_across_boundry_for_circular_fragment(self):
s1 = 'atcggtatctactatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1, circular=True)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = (s1[-10:] + s1[0:10]) + 'ttttttttttt'
res = blast_genome(g1, 'blastn', query)
# we are not removing redundant matches when matching across circular
# boundaries, since blasting across circular boundary of a genome is a
# rare case. so in this particular case, you will find two results, one
# for the end of the query at the start of the genome, one for across
# the circular boundary.
found = False
for r in res:
if r.query_start == 1 and r.query_end == 20:
self.assertEquals(r.fragment_id, f1.id)
self.assertEquals(r.query_start, 1)
self.assertEquals(r.query_end, 20)
self.assertEquals(r.subject_start, len(s1) - 10 + 1)
self.assertEquals(r.subject_end, len(s1) + 10)
self.assertEquals(r.fragment_length, len(s1))
self.assertEquals(r.strand(), 1)
found = True
break
self.assertEquals(found, True)
