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 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_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)