def pcr_from_genome(genome, primer_a_sequence, primer_b_sequence):
"""
PCR on genome, using two primer sequences. Returns tuple of PCR product
sequence, primer a blast results, and primer b blast results. Produuct
sequence may be None if primers do not bind unique or in a way that can
result in a PCR product.
A PCR can create a product if each primer uniquely binds to the genome,
primers bind to the same fragment, on sense and antisense strands
respectively, and non-overlapping in their sense strand binding positions
"""
primer_a_results = blast_genome(genome, 'blastn', primer_a_sequence)
primer_b_results = blast_genome(genome, 'blastn', primer_b_sequence)
pcr_products = []
for a_res in primer_a_results:
for b_res in primer_b_results:
product = compute_pcr_product(primer_a_sequence, a_res,
primer_b_sequence, b_res)
if product is not None:
pcr_products.append(product)
if len(pcr_products) == 1:
product = pcr_products[0][0]
region = pcr_products[0][1]
return (product, primer_a_results, primer_b_results,
dict(region=region['region'],
fragment_name=region['fragment'].name,
fragment_id=region['fragment'].id))
else:
return (None, primer_a_results, primer_b_results, None)
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_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 get_cassette_inherited_annotations(genome, cassette, fragment_id,
region_start, region_end):
# blast cassette against unmodified genome
cassette_blast_res = blast_genome(genome, 'blastn', cassette)
# find matches inside region to be replaced
matches = [
res for res in cassette_blast_res if res.fragment_id == fragment_id
and res.subject_start >= region_start and res.subject_end <= region_end
]
inherited_annotations = []
for blast_res in matches:
# get annotations for each match
annotations = blast_result_annotations(blast_res)
# print blast_res.to_dict()
# print annotations
# update annotations with blast result
for annotation in annotations:
inherited_annotations.append(
get_annotation_on_cassette(annotation, blast_res))
return inherited_annotations
def find_possible_swap_regions(genome, front_arm_sequence, back_arm_sequence):
"""
Computes all possible recombined region from arm sequences.
"""
front_arm_results = blast_genome(genome, 'blastn', front_arm_sequence)
back_arm_results = blast_genome(genome, 'blastn', back_arm_sequence)
regions = []
for a_res in front_arm_results:
for b_res in back_arm_results:
region = compute_swap_region_from_results(front_arm_sequence, a_res,
back_arm_sequence, b_res)
if region is not None:
regions.append(region)
return regions
def find_possible_swap_regions(genome, front_arm_sequence, back_arm_sequence, cassette):
"""
Computes all possible recombined region from arm sequences.
"""
front_arm_results = blast_genome(genome, 'blastn', front_arm_sequence)
back_arm_results = blast_genome(genome, 'blastn', back_arm_sequence)
regions = []
for a_res in front_arm_results:
for b_res in back_arm_results:
region = compute_swap_region_from_results(front_arm_sequence, a_res,
back_arm_sequence, b_res,
cassette)
if region is not None:
regions.append(region)
return regions
def on_post(self, request, genome_id):
from edge.blast import blast_genome
genome = get_genome_or_404(genome_id)
parser = RequestParser()
parser.add_argument('query', field_type=str, required=True, location='json')
parser.add_argument('program', field_type=str, required=True, location='json')
args = parser.parse_args(request)
results = blast_genome(genome, args['program'], args['query'])
results = [r.to_dict() for r in results]
return results, 200
def pcr_from_genome(genome, primer_a_sequence, primer_b_sequence):
"""
PCR on genome, using two primer sequences. Returns tuple of PCR product
sequence, primer a blast results, and primer b blast results. Produuct
sequence may be None if primers do not bind unique or in a way that can
result in a PCR product.
A PCR can create a product if each primer uniquely binds to the genome,
primers bind to the same fragment, on sense and antisense strands
respectively, and non-overlapping in their sense strand binding positions
"""
primer_a_results = blast_genome(genome, 'blastn', primer_a_sequence)
primer_b_results = blast_genome(genome, 'blastn', primer_b_sequence)
pcr_products = []
uniq_products = {}
for a_res in primer_a_results:
for b_res in primer_b_results:
product = compute_pcr_product(primer_a_sequence, a_res,
primer_b_sequence, b_res)
if product is not None:
k = (product[0], a_res.fragment_id)
if k not in uniq_products:
pcr_products.append(product)
uniq_products[k] = product
if len(pcr_products) == 1:
product = pcr_products[0][0]
region = pcr_products[0][1]
return (product, primer_a_results, primer_b_results,
dict(region=region['region'],
fragment_name=region['fragment'].name,
fragment_id=region['fragment'].id))
else:
return (None, primer_a_results, primer_b_results, None)
def find_crispr_target(genome, guide, pam):
"""
Find sequences on genome that have exact match to guide, followed by pam
sequence.
"""
guide_matches = blast_genome(genome, 'blastn', guide)
targets = []
for res in guide_matches:
if res.query_start == 1 and res.query_end == len(guide):
target = target_followed_by_pam(res, pam)
if target is not None:
targets.append(target)
return targets
def find_crispr_target(genome, guide, pam):
"""
Find sequences on genome that have exact match to guide, followed by pam
sequence.
"""
guide_matches = blast_genome(genome, 'blastn', guide)
targets = []
for res in guide_matches:
if res.query_start == 1 and res.query_end == len(guide):
target = target_followed_by_pam(res, pam)
if target is not None:
targets.append(target)
return targets
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_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 on_post(self, request, genome_id):
from edge.blast import blast_genome
from edge.blastdb import check_and_build_genome_db
genome = get_genome_or_404(genome_id)
check_and_build_genome_db(genome)
parser = RequestParser()
parser.add_argument('query',
field_type=str,
required=True,
location='json')
parser.add_argument('program',
field_type=str,
required=True,
location='json')
args = parser.parse_args(request)
results = blast_genome(genome, args['program'], args['query'])
results = [r.to_dict() for r in results]
return results, 200
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 get_cassette_inherited_annotations(genome, cassette, fragment_id, region_start, region_end):
# blast cassette against unmodified genome
cassette_blast_res = blast_genome(genome, 'blastn', cassette)
# find matches inside region to be replaced
matches = [res for res in cassette_blast_res
if res.fragment_id == fragment_id and
res.subject_start >= region_start and res.subject_end <= region_end]
inherited_annotations = []
for blast_res in matches:
# get annotations for each match
annotations = blast_result_annotations(blast_res)
# print blast_res.to_dict()
# print annotations
# update annotations with blast result
for annotation in annotations:
inherited_annotations.append(get_annotation_on_cassette(annotation, blast_res))
return inherited_annotations
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_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_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)
# flake8: noqa
import django
django.setup()
import sys
from edge.models import Genome
from edge.blast import blast_genome
from edge.pcr import pcr_from_genome
genome = Genome.objects.get(pk=36161)
print(genome.fragments.count())
res = blast_genome(genome, "blastn", "ctcacgttactgtggggtggaggggaca")
for r in res:
print("p: %s" % r.evalue)
primer_fwd = "aggaagtgccattccgcctgacctcgtctcactgaccgtctctctcctgagtccgga"
primer_rev = "aaagtgtcaaggtctcacgttactgtggggtggaggggaca"
res = blast_genome(genome, "blastn", primer_fwd)
for r in res:
print("fwd: %s" % r.evalue)
res = blast_genome(genome, "blastn", primer_rev)
for r in res:
print("rev: %s" % r.evalue)
print(pcr_from_genome(genome, primer_fwd, primer_rev))
def pcr_from_genome(genome, primer_a_sequence, primer_b_sequence):
"""
PCR on genome, using two primer sequences. Returns tuple of PCR product
sequence, primer a blast results, and primer b blast results. Produuct
sequence may be None if primers do not bind unique or in a way that can
result in a PCR product.
A PCR can create a product if each primer uniquely binds to the genome,
primers bind to the same fragment, on sense and antisense strands
respectively, and non-overlapping in their sense strand binding positions
"""
primer_a_results = []
primer_a_binding_check_len = []
primer_b_results = []
primer_b_binding_check_len = []
res = blast_genome(genome, 'blastn', primer_a_sequence)
for r in res:
primer_a_results.append(r)
primer_a_binding_check_len.append(len(primer_a_sequence))
res = blast_genome(genome, 'blastn', primer_b_sequence)
for r in res:
primer_b_results.append(r)
primer_b_binding_check_len.append(len(primer_b_sequence))
# checking various binding length
for i in range(MIN_BINDING_LENGTH, BINDING_LENGTH_HI):
p = primer_a_sequence[-i:]
res = blast_genome(genome, 'blastn', p)
for r in res:
primer_a_results.append(r)
primer_a_binding_check_len.append(len(p))
# checking various binding length
for i in range(MIN_BINDING_LENGTH, BINDING_LENGTH_HI):
p = primer_b_sequence[-i:]
res = blast_genome(genome, 'blastn', p)
for r in res:
primer_b_results.append(r)
primer_b_binding_check_len.append(len(p))
pcr_products = []
uniq_products = {}
for a_len, a_res in zip(primer_a_binding_check_len, primer_a_results):
for b_len, b_res in zip(primer_b_binding_check_len, primer_b_results):
product = compute_pcr_product(primer_a_sequence, a_len, a_res,
primer_b_sequence, b_len, b_res)
if product is not None:
k = (product[0], a_res.fragment_id)
if k not in uniq_products:
pcr_products.append(product)
uniq_products[k] = product
if len(pcr_products) == 1:
product = pcr_products[0][0]
region = pcr_products[0][1]
return (product, primer_a_results, primer_b_results,
dict(region=region['region'],
fragment_name=region['fragment'].name,
fragment_id=region['fragment'].id))
else:
return (None, primer_a_results, primer_b_results, None)
def pcr_from_genome(genome, primer_a_sequence, primer_b_sequence):
"""
PCR on genome, using two primer sequences. Returns tuple of PCR product
sequence, primer a blast results, and primer b blast results. Produuct
sequence may be None if primers do not bind unique or in a way that can
result in a PCR product.
A PCR can create a product if each primer uniquely binds to the genome,
primers bind to the same fragment, on sense and antisense strands
respectively, and non-overlapping in their sense strand binding positions
"""
primer_a_results = []
primer_a_binding_check_len = []
primer_b_results = []
primer_b_binding_check_len = []
res = blast_genome(genome, "blastn", primer_a_sequence)
for r in res:
primer_a_results.append(r)
primer_a_binding_check_len.append(len(primer_a_sequence))
res = blast_genome(genome, "blastn", primer_b_sequence)
for r in res:
primer_b_results.append(r)
primer_b_binding_check_len.append(len(primer_b_sequence))
# checking various binding length
for i in range(MIN_BINDING_LENGTH, BINDING_LENGTH_HI):
p = primer_a_sequence[-i:]
res = blast_genome(genome, "blastn", p)
for r in res:
primer_a_results.append(r)
primer_a_binding_check_len.append(len(p))
# checking various binding length
for i in range(MIN_BINDING_LENGTH, BINDING_LENGTH_HI):
p = primer_b_sequence[-i:]
res = blast_genome(genome, "blastn", p)
for r in res:
primer_b_results.append(r)
primer_b_binding_check_len.append(len(p))
pcr_products = []
uniq_products = {}
for a_len, a_res in zip(primer_a_binding_check_len, primer_a_results):
for b_len, b_res in zip(primer_b_binding_check_len, primer_b_results):
product = compute_pcr_product(primer_a_sequence, a_len, a_res,
primer_b_sequence, b_len, b_res)
if product is not None:
k = (product[0], a_res.fragment_id)
if k not in uniq_products:
pcr_products.append(product)
uniq_products[k] = product
if len(pcr_products) == 1:
product = pcr_products[0][0]
region = pcr_products[0][1]
return (
product,
primer_a_results,
primer_b_results,
dict(
region=region["region"],
fragment_name=region["fragment"].name,
fragment_id=region["fragment"].id,
),
)
else:
return (None, primer_a_results, primer_b_results, None)
