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_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_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 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_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_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 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_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_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_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_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_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)
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)
def __test_verification_primers(self, template, middle, cassette, arm_len,
is_reversed):
from edge.pcr import pcr_from_genome
g = self.build_genome(False, template)
r = find_swap_region(g, cassette, arm_len, design_primers=True)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].verification_cassette), 5)
self.assertEquals(len(r[0].verification_front), 5)
self.assertEquals(len(r[0].verification_back), 5)
# cassette verification primers should work on unmodified genome
for primer in r[0].verification_cassette:
p = pcr_from_genome(g, primer['PRIMER_LEFT_SEQUENCE'],
primer['PRIMER_RIGHT_SEQUENCE'])
self.assertNotEqual(p[0], None)
self.assertEquals(p[0].index(middle) >= 0, True)
# front verification primers should NOT produce product
for primer in r[0].verification_front:
p = pcr_from_genome(g, primer['PRIMER_LEFT_SEQUENCE'],
primer['PRIMER_RIGHT_SEQUENCE'])
self.assertEqual(p[0], None)
# back verification primers should NOT produce product
for primer in r[0].verification_back:
p = pcr_from_genome(g, primer['PRIMER_LEFT_SEQUENCE'],
primer['PRIMER_RIGHT_SEQUENCE'])
self.assertEqual(p[0], None)
# do recombination, then try primers again on modified genome
c = recombine(g, cassette, arm_len)
for f in c.fragments.all():
try:
os.unlink(fragment_fasta_fn(f))
except:
pass
build_all_genome_dbs(refresh=True)
# reload to get blastdb
c = Genome.objects.get(pk=c.id)
if is_reversed:
cassette = str(Seq(cassette).reverse_complement())
# cassette verification primers should work on modified genome, finding cassette
for primer in r[0].verification_cassette:
p = pcr_from_genome(c, primer['PRIMER_LEFT_SEQUENCE'],
primer['PRIMER_RIGHT_SEQUENCE'])
self.assertNotEqual(p[0], None)
self.assertEquals(p[0].index(cassette) >= 0, True)
# front verification primers should find a product including front of cassette
for primer in r[0].verification_front:
p = pcr_from_genome(c, primer['PRIMER_LEFT_SEQUENCE'],
primer['PRIMER_RIGHT_SEQUENCE'])
self.assertNotEqual(p[0], None)
self.assertEquals(
p[0].index(cassette[0:edge.recombine.CHECK_JUNCTION_LEFT_DN])
>= 0, True)
# back verification primers should find a product including back of cassette
for primer in r[0].verification_back:
p = pcr_from_genome(c, primer['PRIMER_LEFT_SEQUENCE'],
primer['PRIMER_RIGHT_SEQUENCE'])
self.assertNotEqual(p[0], None)
self.assertEquals(
p[0].index(cassette[-edge.recombine.CHECK_JUNCTION_RIGHT_UP:])
>= 0, True)
def __test_verification_primers(self, template, middle, cassette, arm_len, is_reversed):
from edge.pcr import pcr_from_genome
g = self.build_genome(False, template)
r = find_swap_region(g, cassette, arm_len, design_primers=True)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].verification_cassette), 5)
self.assertEquals(len(r[0].verification_front), 5)
self.assertEquals(len(r[0].verification_back), 5)
# cassette verification primers should work on unmodified genome
for primer in r[0].verification_cassette:
p = pcr_from_genome(g, primer['PRIMER_LEFT_SEQUENCE'], primer['PRIMER_RIGHT_SEQUENCE'])
self.assertNotEqual(p[0], None)
self.assertEquals(p[0].index(middle) >= 0, True)
# front verification primers should NOT produce product
for primer in r[0].verification_front:
p = pcr_from_genome(g, primer['PRIMER_LEFT_SEQUENCE'], primer['PRIMER_RIGHT_SEQUENCE'])
self.assertEqual(p[0], None)
# back verification primers should NOT produce product
for primer in r[0].verification_back:
p = pcr_from_genome(g, primer['PRIMER_LEFT_SEQUENCE'], primer['PRIMER_RIGHT_SEQUENCE'])
self.assertEqual(p[0], None)
# do recombination, then try primers again on modified genome
c = recombine(g, cassette, arm_len)
for f in c.fragments.all():
try:
os.unlink(fragment_fasta_fn(f))
except:
pass
build_all_genome_dbs(refresh=True)
# reload to get blastdb
c = Genome.objects.get(pk=c.id)
if is_reversed:
cassette = str(Seq(cassette).reverse_complement())
# cassette verification primers should work on modified genome, finding cassette
for primer in r[0].verification_cassette:
p = pcr_from_genome(c, primer['PRIMER_LEFT_SEQUENCE'], primer['PRIMER_RIGHT_SEQUENCE'])
self.assertNotEqual(p[0], None)
self.assertEquals(p[0].index(cassette) >= 0, True)
# front verification primers should find a product including front of cassette
for primer in r[0].verification_front:
p = pcr_from_genome(c, primer['PRIMER_LEFT_SEQUENCE'], primer['PRIMER_RIGHT_SEQUENCE'])
self.assertNotEqual(p[0], None)
self.assertEquals(p[0].index(cassette[0:edge.recombine.CHECK_JUNCTION_LEFT_DN]) >= 0,
True)
# back verification primers should find a product including back of cassette
for primer in r[0].verification_back:
p = pcr_from_genome(c, primer['PRIMER_LEFT_SEQUENCE'], primer['PRIMER_RIGHT_SEQUENCE'])
self.assertNotEqual(p[0], None)
self.assertEquals(p[0].index(cassette[-edge.recombine.CHECK_JUNCTION_RIGHT_UP:]) >= 0,
True)
