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 = 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_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 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_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_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_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 setUp(self):
self.sequence = "agttcgaggctga"
self.genome = Genome.create("Foo")
self.fragment = Fragment.create_with_sequence("Bar", self.sequence)
Genome_Fragment(genome=self.genome,
fragment=self.fragment,
inherited=False).save()
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 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_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_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_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 = 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_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_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_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_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)