def test_cut_circular():
from pydna.dseq import Dseq
from Bio.Restriction import BsaI, KpnI, Acc65I, NotI
test = "aaaaaaGGTACCggtctcaaaa"
for i in range(len(test)):
nt = test[i:] + test[:i]
a = Dseq(nt, circular=True).cut(Acc65I)[0] # G^GTACC
assert a.watson.upper() == "GTACCGGTCTCAAAAAAAAAAG"
assert a.crick.upper() == "GTACCTTTTTTTTTTGAGACCG"
assert a.ovhg == -4 # CggtctcaaaaaaaaaaGGTAC
b = Dseq(nt, circular=True).cut(KpnI)[0] # GGTAC^C
assert b.watson.upper() == "CGGTCTCAAAAAAAAAAGGTAC"
assert b.crick.upper() == "CTTTTTTTTTTGAGACCGGTAC"
assert b.ovhg == 4
c = Dseq(nt, circular=True).cut(BsaI)[0] # ggtctcnnn
assert c.watson.upper() == "AAAAAAAAAGGTACCGGTCTCA"
assert c.crick.upper() == "TTTTTGAGACCGGTACCTTTTT"
assert c.ovhg == -4
d = Dseq(nt, circular=True).cut(NotI)
assert d == ()
def test_lcs():
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord as BSeqRecord
from pydna.dseq import Dseq
from pydna.dseqrecord import Dseqrecord
from pydna.seqrecord import SeqRecord
from pydna.seqfeature import SeqFeature
from Bio.SeqFeature import FeatureLocation, ExactPosition
s = SeqRecord(Seq("GGATCC"))
expected = SeqFeature()
expected.__dict__ = {
"location": FeatureLocation(ExactPosition(0),
ExactPosition(6),
strand=1),
"type": "read",
"id": "<unknown id>",
"qualifiers": {
"label": ["sequence"],
"ApEinfo_fwdcolor": ["#DAFFCF"],
"ApEinfo_revcolor": ["#DFFDFF"],
},
}
assert s.lcs("GGATCC", limit=4).__dict__ == expected.__dict__
assert s.lcs(Seq("GGATCC"), limit=4).__dict__ == expected.__dict__
assert (s.lcs(BSeqRecord(Seq("GGATCC"), name="sequence"),
limit=4).__dict__ == expected.__dict__)
assert s.lcs(Dseq("GGATCC"), limit=4).__dict__ == expected.__dict__
assert (s.lcs(Dseqrecord(Dseq("GGATCC"), name="sequence"),
limit=4).__dict__ == expected.__dict__)
assert (s.lcs(Dseqrecord("GGATCC", name="sequence"),
limit=4).__dict__ == expected.__dict__)
def test_Dseq_cutting_adding():
from pydna.dseq import Dseq
from Bio.Restriction import BamHI, PstI, EcoRI
a = Dseq(
"GGATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGGATCC",
"CCTAGGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCCTAGG"[::
-1],
linear=True,
ovhg=0,
)
b = a.cut(BamHI)[1]
assert (
b.watson ==
"GATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG"
)
assert (
b.crick ==
"GATCCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG"
)
c = Dseq(
"nCTGCAGtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGAATTCn",
"nGACGTCagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCTTAAGn"[::
-1],
linear=True,
ovhg=0,
)
f, d, l = c.cut((EcoRI, PstI))
assert (
d.watson ==
"GtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG"
)
assert (
d.crick ==
"AATTCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaCTGCA"
)
e = Dseq(
"nGAATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCAGn",
"nCTTAAGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaGACGTCn"[::
-1],
linear=True,
ovhg=0,
)
f = e.cut((EcoRI, PstI))[1]
assert (
f.watson ==
"AATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCA"
)
assert (
f.crick ==
"GacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG"
)
def test_Dseq_slicing2():
from pydna.dseq import Dseq
from Bio.Restriction import BamHI, EcoRI, KpnI
a = Dseq("aaGGATCCnnnnnnnnnGAATTCccc", circular=True)
assert a.cut(EcoRI, BamHI, KpnI,) == a.cut(
BamHI,
EcoRI,
KpnI,
)[::-1]
def cut_and_religate_Dseq(seq_string, enz, top):
ds = Dseq(seq_string, linear=top)
frags = list(ds.cut(enz))
if not frags:
return
a = frags.pop(0)
for f in frags:
a += f
if not top:
a = a.looped()
assert eq(a, ds)
def test_misc():
from pydna.dseq import Dseq
x = Dseq("ctcgGCGGCCGCcagcggccg", circular=True)
from Bio.Restriction import NotI
a, b = x.cut(NotI)
z = (a + b).looped()
assert z.shifted(5) == x
def test_olaps():
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord as BSeqRecord
from pydna.dseq import Dseq
from pydna.dseqrecord import Dseqrecord
from pydna.seqrecord import SeqRecord
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
s = SeqRecord(Seq("GGATCC",alphabet=IUPACAmbiguousDNA()))
assert "GGATCC" == str(s.olaps("GGATCC", limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(Seq("GGATCC",alphabet=IUPACAmbiguousDNA()), limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(BSeqRecord(Seq("GGATCC",alphabet=IUPACAmbiguousDNA())), limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(Dseq("GGATCC",alphabet=IUPACAmbiguousDNA()), limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(Dseqrecord(Dseq("GGATCC")), limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(Dseqrecord("GGATCC"), limit = 4)[0].seq)
def test_shifted():
from pydna.dseq import Dseq
a = Dseq("gatc", circular=True)
assert a.shifted(1) == Dseq("atcg", circular=True)
assert a.shifted(4) == a
b = Dseq("gatc", circular=False)
with pytest.raises(TypeError):
b.shifted(1)
def from_SeqRecord(cls,
record: _SeqRecord,
*args,
linear=True,
circular=False,
n=5e-14,
**kwargs):
obj = cls.__new__(cls) # Does not call __init__
obj._seq = _Dseq.quick(
str(record.seq),
_rc(str(record.seq)),
ovhg=0,
linear=linear,
circular=circular,
)
obj.id = record.id
obj.name = record.name
obj.description = record.description
obj.dbxrefs = record.dbxrefs
obj.annotations = {"molecule_type": "DNA"}
obj.annotations.update(record.annotations)
obj._per_letter_annotations = record._per_letter_annotations
obj.features = record.features
obj.map_target = None
obj.n = n
return obj
def from_string(cls,
record: str = "",
*args,
linear=True,
circular=False,
n=5e-14,
**kwargs):
# def from_string(cls, record:str="", *args, linear=True, circular=False, n = 5E-14, **kwargs):
obj = cls.__new__(cls) # Does not call __init__
obj._seq = _Dseq.quick(record,
_rc(record),
ovhg=0,
linear=linear,
circular=circular)
obj.id = _pretty_str("id")
obj.name = _pretty_str("name")
obj.description = _pretty_str("description")
obj.dbxrefs = []
obj.annotations = {"molecule_type": "DNA"}
obj._per_letter_annotations = {}
obj.features = []
obj.map_target = None
obj.n = n
obj.__dict__.update(kwargs)
return obj
def test_Dseq_arguments():
from pydna.dseq import Dseq
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = Dseq(str(f0.seq))
r = Dseq(str(r0.seq))
t = Dseq(str(t0.seq))
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_add_feature():
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord as BSeqRecord
from pydna.dseq import Dseq
from pydna.dseqrecord import Dseqrecord
from pydna.seqrecord import SeqRecord
s = SeqRecord("tttGGATCCaaa")
s.add_feature(3, 9)
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq="GGATCC")
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=Seq("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=Dseq("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=SeqRecord("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=BSeqRecord("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=Dseqrecord("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
with pytest.raises(TypeError):
s.add_feature(seq=Dseqrecord("GGGGGG"))
s = SeqRecord("tttATGaaaTAAggg")
s.add_feature(3, 12)
assert s.features[0].qualifiers["label"] == ["orf9"]
from Bio.Seq import Seq
from pydna.seqrecord import SeqRecord
a = SeqRecord(Seq("atgtaa"))
a.add_feature(2, 4)
assert (
a.list_features() ==
"+-----+---------------+-----+-----+-----+-----+------+------+\n| Ft# | Label or Note | Dir | Sta | End | Len | type | orf? |\n+-----+---------------+-----+-----+-----+-----+------+------+\n| 0 | L:ft2 | --> | 2 | 4 | 2 | misc | no |\n+-----+---------------+-----+-----+-----+-----+------+------+"
)
a.features[0].qualifiers
del a.features[0].qualifiers["label"]
assert (
a.list_features() ==
"+-----+---------------+-----+-----+-----+-----+------+------+\n| Ft# | Label or Note | Dir | Sta | End | Len | type | orf? |\n+-----+---------------+-----+-----+-----+-----+------+------+\n| 0 | nd | --> | 2 | 4 | 2 | misc | no |\n+-----+---------------+-----+-----+-----+-----+------+------+"
)
a.features[0].qualifiers["note"] = ["AwesomeFeature"]
assert (
a.list_features() ==
"+-----+------------------+-----+-----+-----+-----+------+------+\n| Ft# | Label or Note | Dir | Sta | End | Len | type | orf? |\n+-----+------------------+-----+-----+-----+-----+------+------+\n| 0 | N:AwesomeFeature | --> | 2 | 4 | 2 | misc | no |\n+-----+------------------+-----+-----+-----+-----+------+------+"
)
def test_Dseq_slicing():
from pydna.dseq import Dseq
from pydna.readers import read
from pydna.utils import eq
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord as Srec
from Bio.Restriction import BamHI
a = Dseq("ggatcc", "ggatcc", 0)
assert a[:].watson == a.watson
assert a[:].crick == a.crick
assert a.ovhg == a[:].ovhg
b, c = a.cut(BamHI)
d = b[1:5]
e = d.rc()
#assert d+e == Dseq("gatc","gatc",0)
assert e + d == Dseq("gatc", "gatc", 0)
def tester(i, fwd, rev, overhang=None):
print("Test#%d:" % (i))
a = Dseq(fwd, rev, ovhg=overhang)
print(a.fig())
print(a.five_prime_end())
print(a.three_prime_end())
a = DSeq(fwd, rev, overhang=overhang)
print(a.alignment.reference_start, a.alignment.reference_end)
print(a.highlight())
print(a.five_prime_end())
print(a.three_prime_end())
print(a.alignment.read_start, a.alignment.read_end)
print('')
return i + 1
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 toDSEQ(self, graph, edges, nodes):
complements = self.generateComplements(nodes)
dna = []
offset = -10
for edge in edges:
seq = Dseq(edges[edge], complements[edge[1]], ovhg=offset)
x = Dseqrecord(seq)
x.name = edge[0] + "_" + edge[1]
x.seq = seq
dna.append(x)
return dna
def tester(i, fwd, rev, overhang=None):
print("Test#%d:" % (i))
a = Dseq(fwd, rev, ovhg=overhang)
print(a.fig())
print(a.five_prime_end())
print(a.three_prime_end())
a = DSeq(fwd, rev, overhang=overhang)
print(a.alignment.reference_start, a.alignment.reference_end)
print(a.highlight())
print(a.five_prime_end())
print(a.three_prime_end())
print(a.alignment.read_start, a.alignment.read_end)
print('')
return i + 1
def makeDseqFromDF(part, partslist, col="part"):
"""looks up the part named "part" in the column specified as col, and
converts it into a pydna object."""
pseq = partslist[partslist[col] == part].sequence.iloc[0].lower()
pcirc = partslist[partslist[col] == part].circular.iloc[0]
p5pover = int(partslist[partslist[col] == part]["5pend"].iloc[0])
p3pover = int(partslist[partslist[col] == part]["3pend"].iloc[0])
povhg = int(p5pover)
pseqRC = str(Dseq(pseq).rc()).lower()
if (p5pover > 0):
pseq = pseq[p5pover:]
elif (p5pover < 0):
pseqRC = pseqRC[:p5pover]
if (p3pover < 0):
pseq = pseq[:p3pover]
elif (p3pover > 0):
pseqRC = pseqRC[p5pover:]
pDseq = Dseq(pseq, pseqRC, ovhg=povhg)
#this defines a dsdna linear sequence
if (pcirc):
#this makes the sequence circular, if we have to
pDseq = pDseq.looped()
return pDseq
def test_cut_with_no_enzymes():
from pydna.dseq import Dseq
x = Dseq("ctcgGCGGCCGCcagcggccg")
assert x.cut([]) == ()
x = Dseq("ctcgGCGGCCGCcagcggccg", circular=True)
assert x.cut([]) == ()
def chewback(seqtochew, chewamt, end="fiveprime"):
"""chews back the amount mentioned, from the end mentioned."""
wat = seqtochew.watson
cri = seqtochew.crick
if (len(seqtochew) > chewamt * 2 + 1):
if (end == "fiveprime"):
cwat = wat[chewamt:]
ccri = cri[chewamt:]
else:
cwat = wat[:-chewamt]
ccri = cri[:-chewamt]
newseq = Dseq(cwat, ccri, ovhg=chewamt)
return newseq
else:
return None
def test_cut_missing_enzyme():
from pydna.dseq import Dseq
x = Dseq("ctcgGCGGCCGCcagcggccg")
from Bio.Restriction import PstI
assert x.cut(PstI) == ()
x = Dseq("ctcgGCGGCCGCcagcggccg", circular=True)
assert x.cut(PstI) == ()
def plotpcr(template, p1, p2): #p1 is forward, p2 is reverse
template = str.lower(template.replace(' ', ''))
p1 = str.lower(p1.replace(' ', ''))
p2 = str.lower(p2.replace(' ', ''))[::-1]
r_template = str(Dseq(template).reverse_complement())[::-1]
L = len(template)
n_seg = 100
n_sep = 120
i_end = np.append(np.arange(n_seg, L, n_seg), L)
indicator_pos = generate_indicator(template)
seq_show = ''
pf = template.find(p1) + 1
pr = r_template.find(p2) + 1
# primer_f_seq_show = ''
# primer_r_seq_show = ''
for i, n_end in enumerate(i_end):
if (pf >= i * n_seg) and (pf < n_end): # in that range
if (len(p1) <= n_end - pf): #not exceed a row
primer_f_seq_show = '.' * (
pf - 1 - 3 - i * n_seg) + "5'-" + p1 + "-3'-->>dir" + '\n'
template_seq = primer_f_seq_show + template[i *
n_seg:n_end] + '\n'
seq_show += template_seq + indicator_pos[i] + '\n'
# seq_show += '-' * n_seg + '\n'
else: #not in range
template_seq = template[i * n_seg:n_end] + '\n'
seq_show += template_seq + indicator_pos[i] + '\n'
# seq_show += '-' * n_seg + '\n'
if (pr >= i * n_seg) and (pr < n_end):
if (len(p2) <= n_end - pr):
primer_r_seq_show = '.' * (
pr - i * n_seg - 10) + "dir<<-3'-" + p2 + "-5'" + '\n'
r_template_seq = r_template[i * n_seg:n_end] + '\n'
seq_show += r_template_seq + '\n' + primer_r_seq_show
seq_show += '-' * n_sep + '\n'
else:
seq_show += r_template[i * n_seg:n_end] + '\n' + '-' * n_sep + '\n'
return seq_show
def test_Dseq___getitem__():
from pydna.dseq import Dseq
s = Dseq("GGATCC", circular=False)
assert s[1:-1] == Dseq("GATC", circular=False)
t = Dseq("GGATCC", circular=True)
assert t[1:5] == Dseq("GATC")
assert t[1:5].__dict__ == Dseq("GATC").__dict__
assert s[1:5] == Dseq("GATC")
assert s[1:5] == Dseq("GATC", circular=False)
assert s[5:1:-1] == Dseq("CCTA")
assert t[5:1] == Dseq("CG")
assert s[9:1] == Dseq("")
assert t[9:1] == Dseq("")
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2020 by Björn Johansson. All rights reserved.
# This code is part of the Python-dna distribution and governed by its
# license. Please see the LICENSE.txt file that should have been included
# as part of this package.
"""This module provide most pydna functionality in the local namespace.
Example
-------
>>> from pydna.all import *
>>> Dseq("aaa")
Dseq(-3)
aaa
ttt
>>> Dseqrecord("aaa")
Dseqrecord(-3)
>>> from pydna.all import __all__
>>> __all__
['Anneal', 'pcr', 'Assembly', 'genbank', 'Genbank', 'download_text\
', 'Dseqrecord', 'Dseq', 'read', 'read_primer', 'parse', 'parse_primers\
', 'ape', 'primer_design', 'assembly_fragments', 'circular_assembly_fragments\
', 'eq', 'gbtext_clean', 'primerlist']
>>>
"""
__all__ = [
"Anneal",
"pcr",
"Assembly",
def test_repr():
from pydna.dseq import Dseq
a = Dseq("gattcgtatgctgatcgtacgtactgaaaac")
assert repr(a) == 'Dseq(-31)\ngatt..aaac\nctaa..tttg'
b = Dseq("gattcgtatgctgatcgtacgtactgaaaac", "gactagcatgcatgacttttc"[::-1])
assert repr(b) == 'Dseq(-31)\ngattcgtatgctga..aaac\n gact..tttc'
c = Dseq("gattcgtatgctgatcgtacgtactgaaaac", "actagcatgcatgacttttc"[::-1])
assert repr(c) == 'Dseq(-31)\ngatt..atgctgat..aaac\n acta..tttc'
d = Dseq("gattcgtatgctgatcgtacg", "gactagcatgc"[::-1])
assert repr(d) == 'Dseq(-21)\ngattcgtatgctgatcgtacg\n gactagcatgc'
e = Dseq("gactagcatgcatgacttttc", "gattcgtatgctgatcgtacgtactgaaaac"[::-1])
assert repr(e) == 'Dseq(-31)\n gact..tttc\ngattcgtatgctga..aaac'
f = Dseq("Ggactagcatgcatgacttttc", "gattcgtatgctgatcgtacgtactgaaaac"[::-1])
assert repr(f) == 'Dseq(-31)\n Ggac..tttc\ngattcgtatgctg..aaac'
g = Dseq("gattcgtatgctgatcgtacgtactgaaaac", "ctaagcatacgactagc"[::-1])
assert repr(g) == 'Dseq(-31)\ngatt..atcgtacg..aaac\nctaa..tagc '
h = Dseq("cgtatgctgatcgtacgtactgaaaac", "gcatacgactagc"[::-1])
assert repr(h) == 'Dseq(-27)\ncgtatgctgatcgtacgtactgaaaac\ngcatacgactagc'
i = Dseq("cgtatgctgatcgtacgtactgaaaacagact", "gcatacgactagc"[::-1])
assert repr(i) == 'Dseq(-32)\ncgta..atcgtacg..gact\ngcat..tagc '
j = Dseq("gattcgtatgctgatcgtacgtactgaaaac", "acAAGGAGAGAtg", ovhg=11)
assert repr(
j) == 'Dseq(-42)\n gattcg..aaac\ngtAG..GGAAca '
k = Dseq("g", "gattcgtatgctgatcgtacgtactgaaaac", ovhg=0)
assert repr(k) == 'Dseq(-31)\ng \ncaaaa..ttag'
x = Dseq("gattcgtatgctgatcgtacgtactgaaaa")
assert repr(
x
) == 'Dseq(-30)\ngattcgtatgctgatcgtacgtactgaaaa\nctaagcatacgactagcatgcatgactttt'
y = Dseq("gattcgtatgctgatcgtacgtactgaaaa", "gactagcatgcatgactttt"[::-1])
assert repr(
y
) == 'Dseq(-30)\ngattcgtatgctgatcgtacgtactgaaaa\n gactagcatgcatgactttt'
z = Dseq("gattcgtatgctgatcgtacgtactgaaaa", "actagcatgcatgactttt"[::-1])
assert repr(
z
) == 'Dseq(-30)\ngattcgtatgctgatcgtacgtactgaaaa\n actagcatgcatgactttt'
def test_initialization():
import pytest
from pydna.dseq import Dseq
obj = Dseq("a", "t", 0)
assert obj * 3 == Dseq("aaa", "ttt", 0)
assert not obj == 123
assert obj * 0 == Dseq("")
with pytest.raises(TypeError):
obj * 2.3
assert obj.seguid() == "bc1M4j2I4u6VaLpUbAB8Y9kTHBs"
assert obj == Dseq("a", "t", circular=False, linear=True)
with pytest.raises(ValueError):
Dseq("a", ovhg=0)
with pytest.raises(ValueError):
Dseq("ttt", "tt")
with pytest.raises(ValueError):
Dseq("ttt", "aa")
obj2 = Dseq("gata")
assert obj2.linear == True
assert obj2.circular == False
l = Dseq("gt")
c = l.looped()
assert l.linear
assert not l.circular
assert c.circular
assert not c.linear
assert Dseq("gt", linear=None, circular=None) == l
assert Dseq("gt", linear=None, circular=False) == l
assert Dseq("gt", linear=None, circular=True) == c
assert Dseq("gt", linear=False, circular=None) == c
assert Dseq("gt", linear=False, circular=False) == l
assert Dseq("gt", linear=False, circular=True) == c
assert Dseq("gt", linear=True, circular=None) == l
assert Dseq("gt", linear=True, circular=False) == l
assert Dseq("gt", linear=True, circular=True) == l
assert Dseq.from_string("A") == Dseq("A") == Dseq("A", linear=True)
assert (
Dseq.from_string("A", linear=False, circular=True)
== Dseq("A", circular=True)
== Dseq("A", linear=False)
)
def test_repr():
from pydna.dseq import Dseq
a = Dseq("gattcgtatgctgatcgtacgtactgaaaac")
assert repr(a) == "Dseq(-31)\ngatt..aaac\nctaa..tttg"
b = Dseq("gattcgtatgctgatcgtacgtactgaaaac", "gactagcatgcatgacttttc"[::-1])
assert repr(b) == "Dseq(-31)\ngattcgtatgctga..aaac\n gact..tttc"
c = Dseq("gattcgtatgctgatcgtacgtactgaaaac", "actagcatgcatgacttttc"[::-1])
assert repr(c) == "Dseq(-31)\ngatt..atgctgat..aaac\n acta..tttc"
d = Dseq("gattcgtatgctgatcgtacg", "gactagcatgc"[::-1])
assert repr(d) == "Dseq(-21)\ngattcgtatgctgatcgtacg\n gactagcatgc"
e = Dseq("gactagcatgcatgacttttc", "gattcgtatgctgatcgtacgtactgaaaac"[::-1])
assert repr(e) == "Dseq(-31)\n gact..tttc\ngattcgtatgctga..aaac"
f = Dseq("Ggactagcatgcatgacttttc", "gattcgtatgctgatcgtacgtactgaaaac"[::-1])
assert repr(f) == "Dseq(-31)\n Ggac..tttc\ngattcgtatgctg..aaac"
g = Dseq("gattcgtatgctgatcgtacgtactgaaaac", "ctaagcatacgactagc"[::-1])
assert repr(g) == "Dseq(-31)\ngatt..atcgtacg..aaac\nctaa..tagc "
h = Dseq("cgtatgctgatcgtacgtactgaaaac", "gcatacgactagc"[::-1])
assert repr(h) == "Dseq(-27)\ncgtatgctgatcgtacgtactgaaaac\ngcatacgactagc"
i = Dseq("cgtatgctgatcgtacgtactgaaaacagact", "gcatacgactagc"[::-1])
assert repr(i) == "Dseq(-32)\ncgta..atcgtacg..gact\ngcat..tagc "
j = Dseq("gattcgtatgctgatcgtacgtactgaaaac", "acAAGGAGAGAtg", ovhg=11)
assert repr(j) == "Dseq(-42)\n gattcg..aaac\ngtAG..GGAAca "
k = Dseq("g", "gattcgtatgctgatcgtacgtactgaaaac", ovhg=0)
assert repr(k) == "Dseq(-31)\ng \ncaaaa..ttag"
x = Dseq("gattcgtatgctgatcgtacgtactgaaaa")
assert (
repr(x)
== "Dseq(-30)\ngattcgtatgctgatcgtacgtactgaaaa\nctaagcatacgactagcatgcatgactttt"
)
y = Dseq("gattcgtatgctgatcgtacgtactgaaaa", "gactagcatgcatgactttt"[::-1])
assert (
repr(y)
== "Dseq(-30)\ngattcgtatgctgatcgtacgtactgaaaa\n gactagcatgcatgactttt"
)
z = Dseq("gattcgtatgctgatcgtacgtactgaaaa", "actagcatgcatgactttt"[::-1])
assert (
repr(z)
== "Dseq(-30)\ngattcgtatgctgatcgtacgtactgaaaa\n actagcatgcatgactttt"
)
def makeEchoFile(parts,aslist,gga=ggaPD,partsFm=partsFm,source=source,\
output = "output.csv",selenzyme=selenzyme,fname="recentassembly",\
protocolsDF=None,sepfiles=True,sepfilename="outputLDV.csv",printstuff=True,progbar=None):
"""makes an echo csv using the given list of assemblies and source plate of
parts..
inputs:
parts: dataframe of what's in the source plate
aslist: dataframe of what we need to assemble
gga: a short dictionary indicating what volume of all the components
go into the reaction mix
partsFm: how many femtomoles of each part to use
source: the name of the source plate. like "384PP_AQ_BP or something
output: the name of the output file
selenzyme: the enzyme we are going to use for assembly. everything
is assembled with the same enzyme! actually this does nothing because
the enzyme is taken from the aslist thing anyway
fname: this is the name of the folder to save the successfully assembled
dna files into
protocolsDF: a dataframe containing a descriptor for different possible
protocols. For instance it would say how much DNA volume and
concentration we need for GGA or gibson."""
#this is the boilerplate columns list
outfile = "Source Plate Name,Source Plate Barcode,Source Plate Type,Source Well,\
Sample ID,Sample Name,Sample Group,Sample Comment,Destination Plate Name,\
Destination Well,Transfer Volume\n"
outfile2 = "Source Plate Name,Source Plate Barcode,Source Plate Type,Source Well,\
Sample ID,Sample Name,Sample Group,Sample Comment,Destination Plate Name,\
Destination Well,Transfer Volume\n"
f2init = len(outfile2)
#this iterates through rows in the assembly list file. Each row
#defines an assembly, with the columns representing what parts go in.
#this may not be ideal but it's fairly human readable and we only do
#four parts + vector for each assembly.
_, fname = os.path.split(fname)
if ("." in fname):
fname = fname[:fname.index(".")]
#the following is for making a spreadsheet style sequence list for performing further assemblies
prodSeqSpread = "well,part,description,type,left,right,conc (nM),date,numvalue,sequence,circular,5pend,3pend,length\n"
prevplate = None
prevtype = None
maxprog = float(len(aslist))
for assnum in range(len(aslist)):
if (progbar != None):
progbar.value = float(assnum + 1) / maxprog
assembly = aslist[assnum:assnum + 1] #cuts out one row of dataframe
dwell = assembly.targwell[
assembly.targwell.index[0]] #well where assembly will happen
#print("pick enzyme")
#print(assembly)
try:
selenzyme = assembly.enzyme[assembly.enzyme.index[0]]
#if the user forgot to define an enzyme assume it is BsaI. That's the most common one we use
except KeyError:
selenzyme = "BsaI"
if (protocolsDF != None):
cprt_temp = "gga"
if (selenzyme == "gibson"):
cprt_temp = "gibson"
curprot = {"dnasln": protocolsDF[(protocolsDF.protocol==cprt_temp)&\
(protocolsDF.component == "dnasln")].amount.iloc[0]}
partsFm = curprot[curprot.component == partfm].amount.iloc[0]
vectorFm = curprot[curprot.component == vectorfm].amount.iloc[0]
else:
curprot = ggaPD
partsFm = ggaFm
vectorFm = ggavecGm
if (selenzyme == "gibson"):
curprot = gibassyPD
partsFm = gibFm
vectorFm = gibvecFm
water = float(curprot[curprot.component == "dnasln"].volume
) * 1000 #total amount of water, to start with
if (printstuff):
print("assembling with " + selenzyme)
aind = assembly.index[
0] #necessary for dataframes probably because I'm dumb
frags = []
if (not selenzyme == "gibson"):
enzyme = enzymes[selenzyme]
esite = enzyme.site.lower()
esiterc = str(Dseq(enzyme.site).rc()).lower()
for col in assembly:
if (col == "targwell"
): #since every row is terminated by the "target well",
#we'll take this opportunity to put in the water
if (int(water) < 25):
#echo gets mad if you tell it to pipet significantly less than 25 nl
water = 25
ewat = int(
water) #the echo automatically rounds to the nearest 25,
#so it's not really necessary to round here.
#dsrfrags = [Dseqrecord(a) for a in frags]
#x = pydAssembly(dsrfrags,limit = 4)
#print(frags)
#print(len(frags))
allprod = []
nefrags = []
cutfrags = []
if (selenzyme != "gibson"):
enzyme = enzymes[selenzyme]
for frag in frags:
if (selenzyme == "gibson"):
if (len(frag) > chewnt * 2 + 1):
nefrags += [chewback(frag, chewnt)]
else:
raise ValueError("part with sequence "+frag+" is too "+\
"short for gibson! (<= 80 nt)")
else:
newpcs = frag.cut(enzyme)
if (len(newpcs) == 0):
newpcs += [frag]
for pcs in newpcs:
if (pcs.find(esite) + pcs.find(esiterc) == -2):
nefrags += [pcs]
allprod = DPallCombDseq(nefrags)
goodprod = []
newpath = os.path.join(dnaPath, fname)
if (printstuff):
print("saving in folder {}".format(newpath))
Cname = ""
try:
#this part gathers the "name" column to create the output sequence
Cname = assembly.name[assembly.name.index[0]]
except KeyError:
Cname = ""
if (Cname == "" or str(Cname) == "nan"):
Cname = "well" + dwell
if (printstuff):
print("Parts in construct {}".format(Cname))
if not os.path.exists(newpath):
if (printstuff):
print("made dirs!")
os.makedirs(newpath)
num = 0
for prod in allprod:
Cnamenum = Cname
if (len(allprod) > 1):
wout = open(
os.path.join(newpath,
Cname + "_" + str(num) + ".gbk"), "w")
Cnamenum = Cname + "_" + str(num)
else:
wout = open(os.path.join(newpath, Cname + ".gbk"), "w")
if (bluntLeft(prod) and bluntRight(prod)):
num += 1
goodprod += [prod]
topo = ["linear", "circular"][int(prod.circular)]
booltopo = ["FALSE", "TRUE"][int(prod.circular)]
#wout.write("\r\n>Construct"+str(num)+"_"+topo)
un_prod = "_".join(Cnamenum.split())
wout.write(
"LOCUS {} {} bp ds-DNA {} SYN 01-JAN-0001\n"
.format(un_prod, len(prod), topo))
wout.write("ORIGIN\n")
wout.write(str(prod) + "\n//")
now = datetime.datetime.now()
nowdate = "{}/{}/{}".format(now.month, now.day,
now.year)
prodSeqSpread += "{},{},assembled with {},,,,30,{},,{},{},{},{},{}\n".format(\
dwell,un_prod, selenzyme,nowdate,prod,booltopo,0,0,len(prod))
wout.close()
assembend = ["y", "ies"][int(len(goodprod) > 1)]
if (printstuff):
print("Detected {} possible assembl{}".format(
len(goodprod), assembend))
frags = []
if (water <= 0):
print("WARNING!!!! water <=0 in well {}".format(dwell))
else:
#print("water from {} to {}, {} nl".format(waterwell,dwell,ewat))
if (prevplate == None):
#print("normalwater")
outfile += echoline(waterwell, dwell, ewat)
else:
#print("platewater")
watline = echoline(waterwell,
dwell,
ewat,
spname=prevplate,
sptype=prevtype,
platebc=prevplate)
if ("LDV" in prevtype):
outfile2 += watline
else:
outfile += watline
#add water to the well!
if (printstuff):
print("")
elif (col == "comment"): #skip this column!
pass
elif (col == "enzyme"):
pass
elif (col == "name"):
pass
else:
part = assembly[col][aind]
#print(assembly[col][aind])
#print("currently on "+part)
#part = assembly[col][aind] #well corresponding to the part we want
if (str(part) == 'nan'):
#this means we skip this part
if (printstuff):
print("skip one!")
else:
part = assembly[col][aind]
#this is the name of the part!
#parts[parts.part==assembly[col][aind]].well.iloc[0]
evol = 0
if (':' in str(part)):
#this means we have multiple parts to mix!
subparts = part.split(':')
t_partsFm = partsFm / len(subparts)
t_vecFm = vectorFm / len(subparts)
for subpart in subparts:
useFm = t_partsFm
if (col == "vector"):
#use the vector at lower concentration!!
useFm = t_vecFm
e1,e2,pDseq,prevplate,prevtype = echoSinglePart(parts,\
subpart,useFm,dwell,printstuff=printstuff)
frags += [pDseq]
evol += e2
if (sepfiles):
if ("LDV" in e1):
outfile2 += e1
else:
outfile += e1
else:
outfile += e1
else:
useFm = partsFm
if (col == "vector"):
#use the vector at lower concentration!!
useFm = vectorFm
e1,e2,pDseq,prevplate,prevtype = echoSinglePart(parts,\
part,useFm,dwell,printstuff=printstuff)
frags += [pDseq]
evol += e2
if (sepfiles):
if ("LDV" in e1):
outfile2 += e1
else:
outfile += e1
else:
outfile += e1
water = water - evol
pspread = open(os.path.join(newpath, fname + ".csv"), "w")
pspread.write(prodSeqSpread)
pspread.close()
seqdispDF = pd.read_csv(os.path.join(newpath, fname + ".csv"),
usecols=["well", "part", "circular", "length"])
display(seqdispDF)
display(FileLink(os.path.join(newpath, fname + ".csv")))
ofle = open(output, "w")
ofle.write(outfile)
ofle.close()
display(FileLink(output))
if (sepfiles and (len(outfile2) > f2init)):
if (printstuff):
print("wrote LDV steps in {}".format(sepfilename))
ofle2 = open(sepfilename, "w")
ofle2.write(outfile2)
ofle2.close()
display(FileLink(sepfilename))
def DPallCombDseq(partslist):
'''Finds all paths through the partsist using a graph type of approach.
First a graph is constructed from all possible overhang interactions,
then the program makes paths from every part to a logical conclusion
in the graph, then it backtracks and actually assembles the DNA.'''
#actually, we need to produce a graph which describes the parts FIRST
#then, starting from any part, traverse the graph in every possible path and store
#the paths which are "valid" i.e., produce blunt ended or circular products.
edgeDict = defaultdict(
lambda: []) #dictionary of all edges in the partslist!
nodeDict = {} #defaultdict(lambda : [])
partDict = {} #defaultdict(lambda : [])
pind = 0
for part in partslist:
Lend = ""
Rend = ""
Ltype, Lseq = part.five_prime_end()
Rtype, Rseq = part.three_prime_end()
if (Ltype == "blunt"):
Lend = "blunt"
edgeDict[Lend].append([pind, 0])
#pushDict(edgeDict,Lend,((pind,0),))
else:
if (Ltype == "3'"):
Lend = str(Dseq(Lseq).rc()).lower()
else:
Lend = str(Lseq).lower()
edgeDict[Lend].append([pind, 0])
#pushDict(edgeDict,Lend,((pind,0),))
if (Rtype == "blunt"):
Rend = "blunt"
edgeDict[Rend].append([pind, 1])
#pushDict(edgeDict,Rend,((pind,1),))
else:
if (Rtype == "5'"):
Rend = str(Dseq(Rseq).rc()).lower()
else:
Rend = str(Rseq).lower()
edgeDict[Rend].append([pind, 1])
#pushDict(edgeDict,Rend,((pind,1),))
nodeDict[pind] = (Lend, Rend)
pind += 1
paths = []
for pind in list(nodeDict.keys()):
paths += findDNAPaths(pind, nodeDict, edgeDict)
goodpaths = []
#print("paths are {}".format(paths))
for path in paths:
#print("path is")
#print(path)
fpart = path[0]
rpart = path[-1]
npart = False
if (nodeDict[fpart][0] == "blunt" and nodeDict[rpart][1] == "blunt"):
#this means we have a blunt ended path! good
npart = True
accpart = partslist[fpart]
for pind in path[1:]:
accpart += partslist[pind]
elif (nodeDict[fpart][0] == nodeDict[rpart][1]):
npart = True
#this means we have a circular part! also good!
accpart = partslist[fpart]
for pind in path[1:]:
accpart += partslist[pind]
accpart = accpart.looped()
if (npart):
if (isNewDseq(accpart, goodpaths)):
goodpaths += [accpart]
return goodpaths
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,
})