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 test_dseq():
import textwrap
from pydna.dseq import Dseq
obj1 = Dseq("a", "t", circular=True)
obj2 = Dseq("a", "t")
with pytest.raises(TypeError):
obj1 + obj2
with pytest.raises(TypeError):
obj2 + obj1
with pytest.raises(TypeError):
obj1 + ""
with pytest.raises(AttributeError):
obj2 + ""
obj1 = Dseq("at", "t")
obj2 = Dseq("a", "t")
with pytest.raises(TypeError):
obj1 + obj2
obj = Dseq("aaa", "ttt", circular=True)
assert obj[1:2] == Dseq("a", "t", 0)
assert obj[:] == Dseq("aaa", "ttt", circular=False)
obj = Dseq("atg", "cat", 0, circular=False)
assert obj[1:2]._data == "atg"[1:2]
assert obj[2:1]._data == "atg"[2:1]
assert obj.reverse_complement() == obj.rc() == Dseq("cat", "atg", 0)
obj = Dseq("atg", "cat", circular=True)
assert obj.looped() == obj
assert obj[:] == Dseq("atg", "cat", 0, circular=False)
assert obj[1:2]._data == "atg"[1:2]
assert obj[2:1]._data == "ga"
obj = Dseq("G", "", 0)
assert obj.five_prime_end() == ("5'", "g")
obj = Dseq("", "C", 0)
assert obj.five_prime_end() == ("3'", "c")
obj = Dseq("ccGGATCC", "aaggatcc", -2)
assert obj._data == "ccGGATCCtt"
assert str(obj.mung()) == "GGATCC"
rpr = textwrap.dedent(
"""
Dseq(-10)
ccGGATCC
cctaggaa
"""
).strip()
assert repr(obj) == rpr
assert obj[3] == Dseq("G", "c", 0)
assert obj.fill_in() == Dseq("ccGGATCCtt", "aaggatccgg", 0)
assert obj + Dseq("") == obj
assert Dseq("") + obj == obj
obj = Dseq("gatcAAAAAA", "gatcTTTTTT")
assert obj.fill_in("gatc") == Dseq("gatcAAAAAAgatc", "gatcTTTTTTgatc")
assert obj.fill_in("atc") == obj
assert obj.fill_in("ac") == obj
assert obj.fill_in("at") == obj
obj = Dseq("AAAAAAgatc", "TTTTTTgatc")
assert obj.fill_in("gatc") == obj
assert obj.fill_in("atc") == obj
assert obj.fill_in("ac") == obj
assert obj.fill_in("at") == obj
obj = Dseq("gatcAAAAAA", "gatcTTTTTT")
assert obj.t4() == Dseq("gatcAAAAAAgatc", "gatcTTTTTTgatc")
assert obj.t4("at") == obj
assert obj.t4("atg") == Dseq("gatcAAAAAAgat", "gatcTTTTTTgat")
assert obj.t4("atgc") == Dseq("gatcAAAAAAgatc", "gatcTTTTTTgatc")
assert obj.mung() == Dseq("AAAAAA", "TTTTTT")
obj = Dseq("AAAAAAgatc", "TTTTTTgatc")
assert obj.t4() == obj.t4("at") == Dseq("AAAAAA")
assert obj.t4("atc") == obj.t4("atg") == obj.t4("atcg") == Dseq("AAAAAA")
assert Dseq("GGATCC", "GGATCC").t4() == Dseq("GGATCC", "GGATCC")
assert Dseq("GGATCCa", "GGATCC").t4() == Dseq("GGATCC", "GGATCC")
assert Dseq("aGGATCC", "GGATCC").t4() == Dseq("aGGATCC", "GGATCCt")
assert Dseq("aGGATCCa", "GGATCC").t4() == Dseq("aGGATCC", "GGATCCt")
assert Dseq("GGATCC", "aGGATCC").t4() == Dseq("GGATCCt", "aGGATCC")
assert Dseq("GGATCC", "GGATCCa").t4() == Dseq("GGATCC", "GGATCC")
assert Dseq("GGATCC", "aGGATCCa").t4() == Dseq("GGATCCt", "aGGATCC")
assert Dseq("GGATCC", "ATCC").t4("g") == Dseq("gg", "", ovhg=0)
assert Dseq("GGATCC", "GGATCC").t4("gat") == Dseq("ggat", "ggat", ovhg=-2)
a2 = Dseq("ccGGATCCaa", "ggatcc", -2)
assert a2._data == "ccGGATCCaa"
assert a2._data == "ccGGATCCaa"
assert str(a2.mung()) == "GGATCC"
rpr = textwrap.dedent(
"""
Dseq(-10)
ccGGATCCaa
cctagg
"""
).strip()
assert repr(a2) == rpr
a3 = Dseq("ccGGATCC", "ggatcc", -2)
assert a3._data == "ccGGATCC"
assert a3._data == "ccGGATCC"
assert str(a3.mung()) == "GGATCC"
rpr = textwrap.dedent(
"""
Dseq(-8)
ccGGATCC
cctagg
"""
).strip()
assert repr(a3) == rpr
b = Dseq("GGATCC", "aaggatcccc", 2)
assert b._data == "ggGGATCCtt"
assert b._data == "ggGGATCCtt"
assert str(b.mung()) == "GGATCC"
rpr = textwrap.dedent(
"""
Dseq(-10)
GGATCC
cccctaggaa
"""
).strip()
assert repr(b) == rpr
b2 = Dseq("GGATCCaa", "ggatcccc", 2)
assert b2._data == "ggGGATCCaa"
assert b2._data == "ggGGATCCaa"
assert str(b2.mung()) == "GGATCC"
rpr = textwrap.dedent(
"""
Dseq(-10)
GGATCCaa
cccctagg
"""
).strip()
assert repr(b2) == rpr
assert b2.seguid() == "hPNrcQ0sluXyfu4XuUh1trsnygc"
b3 = Dseq("GGATCC", "ggatcccc", 2)
assert b3._data == "ggGGATCC"
assert b3._data == "ggGGATCC"
assert str(b3.mung()) == "GGATCC"
rpr = textwrap.dedent(
"""
Dseq(-8)
GGATCC
cccctagg
"""
).strip()
assert repr(b3) == rpr
c = Dseq("GGATCCaaa", "ggatcc", 0)
assert c._data == "GGATCCaaa"
assert c._data == "GGATCCaaa"
assert str(c.mung()) == "GGATCC"
rpr = textwrap.dedent(
"""
Dseq(-9)
GGATCCaaa
cctagg
"""
).strip()
assert repr(c) == rpr
d = Dseq("GGATCC", "aaaggatcc", 0)
assert d._data == "GGATCCttt"
assert d._data == "GGATCCttt"
assert str(d.mung()) == "GGATCC"
rpr = textwrap.dedent(
"""
Dseq(-9)
GGATCC
cctaggaaa
"""
).strip()
assert repr(d) == rpr
obj = Dseq("GGATCCaaa", "ggatcc", 0)
from Bio.Restriction import BamHI
frag1 = Dseq("G", "gatcc", 0)
frag2 = Dseq("GATCCaaa", "g", -4)
assert obj.cut(BamHI) == (frag1, frag2)
assert frag1 + frag2 == obj
obj.seguid() == "HtK7-_BmOJw0BmtYE8f1yGdHc0c"
assert frag1.seguid() == "yJkorWG5V2etvSLp6E6QNK-KMlQ"
assert frag2.seguid() == "Aw3buI-N85OztBZAzeGJvXGlwO8"
obj = Dseq("tagcgtagctgtagtatgtgatctggtcta", "tagaccagatcacatactacagctacgcta")
assert (
repr(obj)
== "Dseq(-30)\ntagcgtagctgtagtatgtgatctggtcta\natcgcatcgacatcatacactagaccagat"
)
obj2 = Dseq("tagcgtagctgtagtatgtgatctggtcta")
obj3 = obj = Dseq(
"tagcgtagctgtagtatgtgatctggtcta", "tagaccagatcacatactacagctacgcta", 0
)
assert obj == obj2 == obj3
assert obj.find("ggatcc") == -1
assert obj.find("tgtagta") == 9
obj = Dseq("tagcgtagctgtagtatgtgatctggtctaa", "ttagaccagatcacatactacagctacgcta")
obj = Dseq("tagcgtagctgtagtatgtgatctggtctaa", "CCCttagaccagatcacatactacagctacgcta")
assert repr(obj) == "Dseq(-34)\ntagc..ctaa \natcg..gattCCC"
obj = Dseq("tagcgtagctgtagtatgtgatctggtctaaCCC", "ttagaccagatcacatactacagctacgcta")
assert repr(obj) == "Dseq(-34)\ntagc..ctaaCCC\natcg..gatt "
obj = Dseq("agcgtagctgtagtatgtgatctggtctaa", "ttagaccagatcacatactacagctacgcta")
assert repr(obj) == "Dseq(-31)\n agcg..ctaa\natcgc..gatt"
obj = Dseq("Atagcgtagctgtagtatgtgatctggtctaa", "ttagaccagatcacatactacagctacgcta")
assert repr(obj) == "Dseq(-32)\nAtagc..ctaa\n atcg..gatt"
obj = Dseq(
"tagcgtagctgtagtatgtgatctggtctaa", "tatcgcatcgacatcatacactagaccagatt"[::-1]
)
assert repr(obj) == "Dseq(-32)\n tagc..ctaa\ntatcg..gatt"
assert round(obj.mw(), 1) == 19535.6
obj1 = Dseq(
"tagcgtagctgtagtatgtgatctggtcta",
"tagaccagatcacatactacagctacgcta",
circular=True,
linear=False,
)
obj2 = Dseq(
"tagcgtagctgtagtatgtgatctggtcta",
"tagaccagatcacatactacagctacgcta",
circular=True,
)
obj3 = Dseq(
"tagcgtagctgtagtatgtgatctggtcta", "tagaccagatcacatactacagctacgcta", linear=False
)
assert obj1 == obj2 == obj3
assert obj1.find("ggatcc") == -1
assert obj1.find("tgtagta") == 9
assert (
Dseq(
"tagcgtagctgtagtatgtgatctggtcta", "tagaccagatcacatactacagctacgcta"
).looped()
== obj1
)
from Bio.Restriction import BglII, BamHI
obj = Dseq("ggatcc")
assert BglII in obj.no_cutters()
assert BamHI not in obj.no_cutters()
assert BamHI in obj.unique_cutters()
assert BamHI in obj.once_cutters()
assert BamHI in (obj + obj).twice_cutters()
assert BamHI not in obj.twice_cutters()
assert BamHI in obj.n_cutters(1)
assert BamHI in obj.cutters()
from Bio.Restriction import RestrictionBatch
rb = RestrictionBatch((BamHI, BglII))
assert obj.cut(rb) == obj.cut(BamHI, BglII) == obj.cut(BglII, BamHI)
obj = Dseq("ggatccAGATCT")
assert obj.cut(rb) == obj.cut(BamHI, BglII) == obj.cut(BglII, BamHI)
obj = Dseq("AGATCTggatcc")
assert obj.cut(rb) == obj.cut(BamHI, BglII) == obj.cut(BglII, BamHI)
obj = Dseq("ggatccAGATCT", circular=True)
assert obj.cut(rb) == obj.cut(BamHI, BglII) != obj.cut(BglII, BamHI)
obj = Dseq("AGATCTggatcc", circular=True)
assert obj.cut(rb) == obj.cut(BglII, BamHI) != obj.cut(BamHI, BglII)
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,
})