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test_module_dseq.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pytest
def test_cut1():
from pydna.dseq import Dseq
"""
Acc65I.search(_Seq("GGTACC"))
Out [11]: [2]
012345
GGTACC
CCATGG
KpnI.search(_Seq("GGTACC"))
Out [12]: [6]
"""
from Bio.Restriction import Acc65I, Bsp120I, KpnI, ApaI, TaiI, MaeII
"""
|--||-------||-------||----|
aaaGGTACCcccGGGCCCgggACGTaaa
tttCCATGGgggCCCGGGcccTGCAttt
|------||-------||-----||--|
aaaG GGCCCgggA
tttCCATG GcccTGC Acc65I Bsp120I MaeII
GTACCcccG CGTaaa
GgggCCCGG Attt
| | | | 0 4 13 22
0123456789111111111122222222
012345678901234567
aaaGGTAC CgggACGT
tttC CCGGGccc KpnI ApaI TaiI
0 4 13 21
CcccGGGCC aaa
CATGGgggC TGCAttt
|------||------||------||--|
aaaGGTACCcccGGGCCCgggACGTaaa
tttCCATGGgggCCCGGGcccTGCAttt
|--||-------||-------||----|
"""
lds = Dseq("aaaGGTACCcccGGGCCCgggACGTaaa")
frags = lds.cut((Acc65I, Bsp120I, MaeII))
first, second, third, fourth = frags
assert first + second + third + fourth == lds
# TODO: remove
# assert (first.pos, second.pos, third.pos, fourth.pos) == (0, 4, 13, 22)
frags2 = lds.cut((KpnI, ApaI, TaiI))
first2, second2, third2, fourth2 = frags2
assert first2 + second2 + third2 + fourth2 == lds
# TODO: remove
# assert (first2.pos, second2.pos, third2.pos, fourth2.pos) == (0, 4, 13, 21)
def test_cas9():
from pydna.dseq import Dseq
s = Dseq("gattcatgcatgtagcttacgtagtct")
RNA = "catgcatgtagcttacgtag"
assert slice(0, 21, 1), slice(21, 27, 1) == s.cas9(RNA)
def test_initialization():
import pytest
from pydna.dseq import Dseq
obj = Dseq(b"aaa")
assert obj.crick == "ttt"
assert obj.watson == "aaa"
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() == "ldseguid=ydezQsYTZgUCcb3-adxMaq_Xf8g"
assert obj == Dseq("a", "t", circular=False)
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 not obj2.circular
lin_seq = Dseq("gt")
cir_seq = lin_seq.looped()
assert not lin_seq.circular
assert cir_seq.circular
assert Dseq("gt", circular=False) == lin_seq
assert Dseq("gt", circular=True) == cir_seq
assert Dseq.from_string("A") == Dseq("A")
assert Dseq.from_string("A", circular=True) == Dseq("A", circular=True)
obj3 = Dseq.from_representation(
"""
GGATCC
CCTAGG
"""
)
assert obj3.ovhg == 0
obj3 = Dseq.from_representation(
"""
aGGATCC
CCTAGGg
"""
)
assert obj3.ovhg == -1
obj3 = Dseq.from_representation(
"""
GGATCCg
aCCTAGG
"""
)
assert obj3.ovhg == 1
def test_cut_around_and_religate():
from pydna.dseq import Dseq
from pydna.utils import eq
from Bio.Restriction import KpnI, BamHI, Acc65I
def cut_and_religate_Dseq(seq_string, enz, top):
ds = Dseq(seq_string, circular=not 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)
seqs = [
("aaaGGTACCcccGGTACCCgggGGTACCttt", BamHI, False),
("aaaGGTACCcccGGTACCCgggGGTACCttt", Acc65I, False),
("aaaGGTACCcccGGTACCCgggGGTACCttt", KpnI, False),
("aaaGGTACCcccGGTACCCgggGGTACCttt", Acc65I, True),
("aaaGGTACCcccGGTACCCgggGGTACCttt", KpnI, True),
("aaaGGTACCcccGGTACCCgggGGTACCttt", BamHI, True),
("aaaGGTACCcccGGATCCCgggGGTACCttt", [Acc65I, BamHI], False),
("aaaGGTACCcccGGATCCCgggGGTACCttt", [KpnI, BamHI], False),
("aaaGGTACCcccGGATCCCgggGGTACCttt", [BamHI, Acc65I], False),
("aaaGGTACCcccGGATCCCgggGGTACCttt", [BamHI, KpnI], False),
("aaaGGTACCcccGGATCCCgggGGTACCttt", [Acc65I, BamHI], True),
("aaaGGTACCcccGGATCCCgggGGTACCttt", [KpnI, BamHI], True),
("aaaGGTACCcccGGATCCCgggGGTACCttt", [BamHI, Acc65I], True),
("aaaGGTACCcccGGATCCCgggGGTACCttt", [BamHI, KpnI], True),
]
for s in seqs:
print(s)
sek, enz, lin = s
for i in range(len(sek)):
zek = sek[i:] + sek[:i]
cut_and_religate_Dseq(zek, enz, lin)
def test_Dseq_cutting_adding():
from pydna.dseq import Dseq
from Bio.Restriction import BamHI, PstI, EcoRI
a = Dseq(
"GGATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGGATCC",
"CCTAGGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCCTAGG"[::-1],
ovhg=0,
)
b = a.cut(BamHI)[1]
assert b.watson == "GATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG"
assert b.crick == "GATCCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG"
c = Dseq(
"nCTGCAGtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGAATTCn",
"nGACGTCagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCTTAAGn"[::-1],
ovhg=0,
)
f, d, _ = c.cut((EcoRI, PstI))
assert d.watson == "GtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG"
assert d.crick == "AATTCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaCTGCA"
e = Dseq(
"nGAATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCAGn",
"nCTTAAGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaGACGTCn"[::-1],
ovhg=0,
)
f = e.cut((EcoRI, PstI))[1]
assert f.watson == "AATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCA"
assert f.crick == "GacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG"
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 == b"atg"[1:2]
assert obj[2:1]._data == b"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 == b"atg"[1:2]
assert obj[2:1]._data == b"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 == b"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 == b"ccGGATCCaa"
assert a2._data == b"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 == b"ccGGATCC"
assert a3._data == b"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 == b"ggGGATCCtt"
assert b._data == b"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 == b"ggGGATCCaa"
assert b2._data == b"ggGGATCCaa"
assert str(b2.mung()) == "GGATCC"
rpr = textwrap.dedent(
"""
Dseq(-10)
GGATCCaa
cccctagg
"""
).strip()
assert repr(b2) == rpr
assert b2.seguid() == "ldseguid=F0z-LxHZqAK3HvqQiqjM7A28daE"
assert b2.rc().seguid() == "ldseguid=F0z-LxHZqAK3HvqQiqjM7A28daE"
b3 = Dseq("GGATCC", "ggatcccc", 2)
assert b3._data == b"ggGGATCC"
assert b3._data == b"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 == b"GGATCCaaa"
assert c._data == b"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 == b"GGATCCttt"
assert d._data == b"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
assert obj.seguid() == "ldseguid=qvssQpZe_4SlasGZYdKJSkuvQtc"
assert frag1.seguid() == "ldseguid=jcVhCJ9Aa8aIQdBlkSU_XHTWmDc"
assert frag2.seguid() == "ldseguid=SO1HxaZPDpcj-QffzS-mfF6_eag"
assert frag1.rc().seguid() == "ldseguid=jcVhCJ9Aa8aIQdBlkSU_XHTWmDc"
assert frag2.rc().seguid() == "ldseguid=SO1HxaZPDpcj-QffzS-mfF6_eag"
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,
)
obj2 = Dseq(
"tagcgtagctgtagtatgtgatctggtcta",
"tagaccagatcacatactacagctacgcta",
circular=True,
)
obj3 = Dseq(
"tagcgtagctgtagtatgtgatctggtcta",
"tagaccagatcacatactacagctacgcta",
circular=True,
)
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)
# TODO: address this test change Related to https://github.com/pydna-group/pydna/issues/78
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 test_Dseq_slicing():
from pydna.dseq import Dseq
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 test_Dseq_slicing2():
from pydna.dseq import Dseq
from Bio.Restriction import BamHI, EcoRI, KpnI
a = Dseq("aaGGATCCnnnnnnnnnGAATTCccc", circular=True)
# TODO: address this test change Related to https://github.com/pydna-group/pydna/issues/78
assert a.cut(
EcoRI,
BamHI,
KpnI,
) == a.cut(
BamHI,
EcoRI,
KpnI,
)
def test_Dseq___getitem__():
# test the slicing
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("")
# Indexing of full circular molecule (https://github.com/pydna-group/pydna/issues/161)
s = Dseq("GGATCC", circular=True)
str_seq = str(s)
for shift in range(len(s)):
assert str(s[shift:shift]) == str_seq[shift:] + str_seq[:shift]
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_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_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)
# Shifted with zero gives a copy of the sequence, not the same sequence
assert a.shifted(0) == a
assert a.shifted(0) is not a
def test_looped():
# Looping a circular sequence should return a copy of the sequence
# not the same sequence
from pydna.dseq import Dseq
a = Dseq("gatc", circular=True)
assert a.looped() == a
assert a.looped() is not a
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()
# TODO: address this test change Related to https://github.com/pydna-group/pydna/issues/78
assert z.shifted(-6) == x
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 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 test_transcribe():
from pydna.dseq import Dseq
x = Dseq("ATGAAATAA")
assert str(x.transcribe()) == "AUGAAAUAA"
assert str(x.reverse_complement().transcribe()) == "UUAUUUCAU"
def test_translate():
from pydna.dseq import Dseq
x = Dseq("ATGAAATAA")
assert str(x.translate()) == "MK*"
assert str(x.reverse_complement().translate()) == "LFH"
def test_from_full_sequence_and_overhangs():
from pydna.dseq import Dseq
test_cases = [
(2, 2, "AAAA", "TTTT"),
(-2, 2, "AAAAAA", "TT"),
(2, -2, "AA", "TTTTTT"),
(-2, -2, "AAAA", "TTTT"),
(0, 0, "AAAAAA", "TTTTTT"),
]
for crick_ovhg, watson_ovhg, watson, crick in test_cases:
dseq_1 = Dseq.from_full_sequence_and_overhangs("AAAAAA", crick_ovhg=crick_ovhg, watson_ovhg=watson_ovhg)
dseq_2 = Dseq(watson, crick, ovhg=crick_ovhg, circular=False)
assert dseq_1 == dseq_2
assert dseq_2.watson_ovhg() == watson_ovhg
def test_right_end_position():
from pydna.dseq import Dseq
test_cases = [
("AAA", "TT", (3, 2)),
("AA", "TTT", (2, 3)),
("AAA", "TTT", (3, 3)),
]
for watson, crick, expected in test_cases:
dseq = Dseq(watson, crick, ovhg=0, circular=False)
assert dseq.right_end_position() == expected
def test_left_end_position():
from pydna.dseq import Dseq
test_cases = [
("AAA", "TT", (0, 1), -1),
("AA", "TTT", (1, 0), 1),
("AAT", "TTT", (0, 0), 0),
]
for watson, crick, expected, ovhg in test_cases:
dseq = Dseq(watson, crick, ovhg=ovhg, circular=False)
assert dseq.left_end_position() == expected
def test_apply_cut():
from pydna.dseq import Dseq
from Bio.Restriction import EcoRI, BamHI
seq = Dseq("aaGAATTCaa", circular=False)
# A cut where both sides are None returns the same sequence
assert seq.apply_cut(None, None) == seq
# A cut where one side is None leaves that side intact
EcoRI_cut = ((3, -4), None)
assert seq.apply_cut(None, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs(
"aaGAATT", watson_ovhg=-4, crick_ovhg=0
)
assert seq.apply_cut(EcoRI_cut, None) == Dseq.from_full_sequence_and_overhangs(
"AATTCaa", watson_ovhg=0, crick_ovhg=-4
)
# It respects the original overhang
seq = Dseq.from_full_sequence_and_overhangs("aaGAATTCaa", watson_ovhg=1, crick_ovhg=1)
assert seq.apply_cut(None, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs(
"aaGAATT", watson_ovhg=-4, crick_ovhg=1
)
assert seq.apply_cut(EcoRI_cut, None) == Dseq.from_full_sequence_and_overhangs(
"AATTCaa", watson_ovhg=1, crick_ovhg=-4
)
seq = Dseq.from_full_sequence_and_overhangs("aaGAATTCaa", watson_ovhg=-1, crick_ovhg=-1)
assert seq.apply_cut(None, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs(
"aaGAATT", watson_ovhg=-4, crick_ovhg=-1
)
assert seq.apply_cut(EcoRI_cut, None) == Dseq.from_full_sequence_and_overhangs(
"AATTCaa", watson_ovhg=-1, crick_ovhg=-4
)
# A repeated cut in a circular molecule opens it up
seq = Dseq("aaGAATTCaa", circular=True)
assert seq.apply_cut(EcoRI_cut, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs(
"AATTCaaaaGAATT", watson_ovhg=-4, crick_ovhg=-4
)
# Two cuts extract a subsequence
seq = Dseq("aaGAATTCaaGAATTCaa", circular=True)
EcoRI_cut_2 = ((11, -4), None)
assert seq.apply_cut(EcoRI_cut, EcoRI_cut_2) == Dseq.from_full_sequence_and_overhangs(
"AATTCaaGAATT", watson_ovhg=-4, crick_ovhg=-4
)
# Overlapping cuts should return an error
seq = Dseq("aaGAATTCaa", circular=True)
first_cuts = [
((3, -4), BamHI),
((7, 4), BamHI),
# Spanning the origin
((9, -8), BamHI),
((8, 8), BamHI),
]
overlapping_cuts = [
((4, -4), EcoRI),
((2, -4), EcoRI),
((2, -6), EcoRI),
((8, 4), EcoRI),
((6, 4), EcoRI),
((8, 6), EcoRI),
# Spanning the origin
((7, -8), EcoRI),
((6, 8), EcoRI),
]
for first_cut in first_cuts:
for second_cut in overlapping_cuts:
try:
seq.apply_cut(first_cut, second_cut)
except ValueError as e:
assert e.args[0] == "Cuts by BamHI EcoRI overlap."
else:
print(first_cut, second_cut)
assert False, "Expected ValueError"
# Rotating the sequence, apply the same cut
seq = Dseq("acgtATGaatt", circular=True)
for shift in range(len(seq)):
seq_shifted = seq.shifted(shift)
start = 4 - shift
if start < 0:
start += len(seq)
# Cut with negative ovhg
new_cut = ((start, -3), None)
out = seq_shifted.apply_cut(new_cut, new_cut)
assert str(out) == "ATGaattacgtATG"
# Cut with positive ovhg
start = (start + 3) % len(seq)
new_cut = ((start, 3), None)
out = seq_shifted.apply_cut(new_cut, new_cut)
assert str(out) == "ATGaattacgtATG"
# A blunt cut
start = 4 - shift
new_cut = ((start, 0), None)
out = seq_shifted.apply_cut(new_cut, new_cut)
assert str(out) == "ATGaattacgt"
def test_cutsite_is_valid():
from pydna.dseq import Dseq
from Bio.Restriction import EcoRI, PacI, NmeDI, EcoRV
# Works for circular case
seqs = ["GAATTC", "TTAATTAAC", "GATATC"]
enzs = [EcoRI, PacI, EcoRV]
for seq, enz in zip(seqs, enzs):
dseq = Dseq(seq, circular=True)
for shift in range(len(seq)):
dseq_shifted = dseq.shifted(shift)
(cutsite,) = dseq_shifted.get_cutsites([enz])
assert dseq_shifted.cutsite_is_valid(cutsite)
# Works for overhangs
seqs = ["GAATTC", "TTAATTAA", "GATATC"]
for seq, enz in zip(seqs, enzs):
for ovhg in [-1, 0, 1]:
dseq = Dseq.from_full_sequence_and_overhangs(seq, ovhg, 0)
if ovhg != 0:
assert len(dseq.get_cutsites([enz])) == 0
else:
assert len(dseq.get_cutsites([enz])) == 1
dseq = Dseq.from_full_sequence_and_overhangs(seq, 0, ovhg)
if ovhg != 0:
assert len(dseq.get_cutsites([enz])) == 0
else:
assert len(dseq.get_cutsites([enz])) == 1
# Special cases:
dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 0, 0)
assert len(dseq.get_cutsites([NmeDI])) == 2
# Remove left cutting place
assert len(dseq[2:].get_cutsites([NmeDI])) == 1
# Remove right cutting place
assert len(dseq[:-2].get_cutsites([NmeDI])) == 1
# Remove both cutting places
assert len(dseq[2:-2].get_cutsites([NmeDI])) == 0
# overhang left side
dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", -2, 0)
assert len(dseq.get_cutsites([NmeDI])) == 1
dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 2, 0)
assert len(dseq.get_cutsites([NmeDI])) == 1
# overhang right side
dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 0, 2)
assert len(dseq.get_cutsites([NmeDI])) == 1
dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 0, -2)
assert len(dseq.get_cutsites([NmeDI])) == 1
# overhang both sides
dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 2, 2)
assert len(dseq.get_cutsites([NmeDI])) == 0
dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", -2, -2)
assert len(dseq.get_cutsites([NmeDI])) == 0