def get_prop_primers(primers, vector):
vector_name = vector.name
seq = str.lower(vector.sequence)
seq = Dseq(seq.replace(' ', ''))
L = len(str(seq))
rseq = seq.reverse_complement()
for primer in primers:
primer_nor = primer.sequence.replace(' ', '')
p_seq = Dseq(primer_nor)
p_seq_s = str.lower(str(p_seq)) # all lower case
nt = 'atcgn'
idt_codes_subtract1 = ['icy5', 'icy3', '5biosg', '(am)']
idt_codes_subtract2 = ['dspacer']
idt_codes_subtract3 = ['dbcoteg']
idt_codes_subtract4 = ['biotinteg']
idt_codes_plus1 = ['ds', 'idsp']
Lp_subtract = 0
for s1 in idt_codes_subtract1:
if p_seq_s.find(s1) >= 0:
Lp_subtract += 1
for s2 in idt_codes_subtract2:
if p_seq_s.find(s2) >= 0:
Lp_subtract += 2
for s3 in idt_codes_subtract3:
if p_seq_s.find(s3) >= 0:
Lp_subtract += 3
for s4 in idt_codes_subtract4:
if p_seq_s.find(s4) >= 0:
Lp_subtract += 4
for p1 in idt_codes_plus1:
if p_seq_s.find(p1) >= 0:
Lp_subtract -= 1
Lp = 0
for i in nt:
Lp += p_seq_s.count(i)
Lp = Lp - Lp_subtract
if seq.find(p_seq_s) != -1: # match it
position = seq.find(p_seq_s) + 1
dir = 'forward'
in_vector = True
elif rseq.find(p_seq_s) != -1:
position = rseq.find(p_seq_s) - L - 1
dir = 'reverse'
in_vector = True
else:
position = -1
dir = 'none'
in_vector = False
primer.position = position
primer.dir = dir
primer.in_vector = in_vector
primer.length = Lp
primer.save()
return vector_name, seq, L, position, dir, in_vector
def calpcr(request):
# pbr = Vector.objects.get(name='pbr322')
primers = Primer.objects.all()
vector = primers[0].vector
vector_name = vector.name
seq = str.lower(vector.sequence)
seq = Dseq(seq.replace(' ', ''))
L = len(str(seq))
rseq = seq.reverse_complement()
poss = []
for primer in primers:
p_seq = Dseq(primer.sequence.replace(' ', ''))
p_seq_s = str.lower(str(p_seq)) # all lower case
nt='atcgn'
idt_codes_subtract1 = ['icy5', 'icy3', '5biosg', '(am)']
idt_codes_subtract2 = ['dspacer']
idt_codes_subtract3 = ['dbcoteg']
idt_codes_subtract4 = ['biotinteg']
idt_codes_plus1 = ['ds', 'idsp']
Lp_subtract = 0
for s1 in idt_codes_subtract1:
if p_seq_s.find(s1) >= 0:
Lp_subtract += 1
for s2 in idt_codes_subtract2:
if p_seq_s.find(s2) >= 0:
Lp_subtract += 2
for s3 in idt_codes_subtract3:
if p_seq_s.find(s3) >= 0:
Lp_subtract += 3
for s4 in idt_codes_subtract4:
if p_seq_s.find(s4) >= 0:
Lp_subtract += 4
for p1 in idt_codes_plus1:
if p_seq_s.find(p1) >= 0:
Lp_subtract -= 1
Lp = 0
for i in nt:
Lp += p_seq_s.count(i)
Lp = Lp - Lp_subtract
# Lp = len(p_seq_s)
if seq.find(p_seq_s) != -1: # match it
position = seq.find(p_seq_s) + 1
dir = 'forward'
in_vector = True
elif rseq.find(p_seq_s) != -1:
position = rseq.find(p_seq_s) - L - 1
dir = 'reverse'
in_vector = True
else:
position = -1
dir = 'none'
in_vector = False
primer.position = position
primer.dir = dir
primer.in_vector = in_vector
primer.length = Lp
primer.save()
primers = primers.filter(in_vector=True).order_by('position')
# primers = Primer.objects.all().order_by('-created_at')
primerFilter = PrimerFilter(queryset=primers)
if request.method == 'POST' and 'Search' in request.POST:
primerFilter = PrimerFilter(request.POST, queryset=primers)
L = len(str(seq))
# if request.method == 'POST' and 'cal' in request.POST:
check_box_list = request.POST.getlist("check_box")
if len(check_box_list) == 2:
primer_1 = Primer.objects.get(id=check_box_list[0])
p1_name = primer_1.name
primer_2 = Primer.objects.get(id=check_box_list[1])
p2_name = primer_2.name
if primer_1.dir == 'reverse' and primer_2.dir == 'forward':
pr = primer_1.position
pr_name = primer_1.name
pr_seq = primer_1.sequence
pf = primer_2.position
pf_name = primer_2.name
pf_seq = primer_2.sequence
elif primer_2.dir == 'reverse' and primer_1.dir == 'forward':
pr = primer_2.position
pr_name = primer_2.name
pr_seq = primer_2.sequence
pf = primer_1.position
pf_name = primer_1.name
pf_seq = primer_1.sequence
else:
pr = 0
pf = 0
if abs(pr) >= abs(pf):
L_pcr = -pr - pf
else:
L_pcr = L - pr - pf
show_seq = plotpcr(str(seq), pf_seq, pr_seq)
primer_name = [pf_name] + [pr_name]
primer_position = [pf, pr]
else:
L_pcr = 'You can only select two primers!!'
primer_name = ['','']
show_seq = "can't pcr"
primer_name = [''] + ['']
primer_position = ['x', 'x']
return render(request, template_name='primer/seq.html',
context={'seq': seq, 'L': L, 'primers': primers, 'show_seq': show_seq,
'primerFilter': primerFilter, 'primer_name': primer_name,
'L_pcr': L_pcr, 'vector_name': vector_name, 'primer_position': primer_position,
})
