def test_Dseq_slicing2(self):
from Bio.Restriction import BamHI, EcoRI, KpnI
a = Dseq("aaGGATCCnnnnnnnnnGAATTCccc", circular=True)
self.assertEqual(a.cut(
EcoRI,
BamHI,
KpnI,
), a.cut(
BamHI,
EcoRI,
KpnI,
))
a = Dseqrecord("aaGGATCCnnnnnnnnnGAATTCccc", circular=True)
self.assertEqual(
a.cut(
EcoRI,
BamHI,
KpnI,
)[0].seq,
a.cut(
BamHI,
EcoRI,
KpnI,
)[0].seq)
def test_Dseq_slicing2(self):
from Bio.Restriction import BamHI, EcoRI, KpnI
a = Dseq("aaGGATCCnnnnnnnnnGAATTCccc", circular=True)
self.assertEqual( a.cut(EcoRI, BamHI, KpnI,), a.cut(BamHI, EcoRI, KpnI,))
a = Dseqrecord("aaGGATCCnnnnnnnnnGAATTCccc", circular=True)
self.assertEqual( a.cut( EcoRI, BamHI, KpnI,)[0].seq, a.cut( BamHI, EcoRI, KpnI,)[0].seq)
def cut_and_religate_Dseq(seq_string, enz, top):
ds = Dseq(seq_string, linear=top)
frags = ds.cut(enz)
if not frags:
return
a = frags.pop(0)
for f in frags:
a+=f
if not top:
a=a.looped()
self.assertTrue( eq(a,ds) )
def cut_and_religate_Dseq(seq_string, enz, top):
ds = Dseq(seq_string, linear=top)
frags = ds.cut(enz)
if not frags:
return
a = frags.pop(0)
for f in frags:
a += f
if not top:
a = a.looped()
self.assertTrue(eq(a, ds))
def test_Dseq_slicing(self):
from Bio.Restriction import BamHI
a=Dseq("ggatcc","ggatcc",0)
self.assertEqual( a[:].watson, a.watson )
self.assertEqual( a[:].crick, a.crick )
self.assertEqual( a.ovhg, a[:].ovhg )
b,c = a.cut(BamHI)
d = b[1:5]
e = d.rc()
self.assertEqual( d+e, Dseq("gatc","gatc",0))
def test_Dseq_slicing(self):
from Bio.Restriction import BamHI
a = Dseq("ggatcc", "ggatcc", 0)
self.assertEqual(a[:].watson, a.watson)
self.assertEqual(a[:].crick, a.crick)
self.assertEqual(a.ovhg, a[:].ovhg)
b, c = a.cut(BamHI)
d = b[1:5]
e = d.rc()
self.assertEqual(d + e, Dseq("gatc", "gatc", 0))
def test_Dseq_cutting_adding(self):
from Bio.Seq import Seq
from Bio.Restriction import BamHI,EcoRI, PstI, EcoRV, SmaI
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio.SeqUtils.CheckSum import seguid
from pydna import Dseq
a = Dseq('GGATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGGATCC',
'CCTAGGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCCTAGG'[::-1],
linear=True,
ovhg=0)
b = a.cut(BamHI)[1]
self.assertEqual( b.watson , "GATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG")
self.assertEqual( b.crick , "GATCCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG")
c = Dseq('nCTGCAGtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGAATTCn',
'nGACGTCagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCTTAAGn'[::-1],
linear=True,
ovhg=0)
f,d,l = c.cut((EcoRI, PstI))
self.assertEqual( d.watson , "GtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG")
self.assertEqual( d.crick , "AATTCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaCTGCA")
e = Dseq("nGAATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCAGn",
"nCTTAAGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaGACGTCn"[::-1],
linear=True,
ovhg=0)
f = e.cut((EcoRI,PstI))[1]
self.assertEqual( f.watson ,"AATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCA")
self.assertEqual( f.crick , "GacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG")
''' blunt cloning '''
pUC19 = read("./pUC19.gb")
self.assertFalse( pUC19.linear )
self.assertTrue( len(pUC19) == 2686 )
self.assertTrue( len(pUC19.seq.watson) == 2686 )
self.assertTrue( len(pUC19.seq.crick) == 2686 )
self.assertTrue( pUC19.seq.circular == True)
self.assertTrue( pUC19.seq.linear == False)
pUC19_SmaI = pUC19.cut(SmaI)
self.assertTrue( len(pUC19_SmaI) == 1)
pUC19_SmaI = pUC19_SmaI.pop()
self.assertTrue( pUC19_SmaI.linear )
self.assertTrue( len(pUC19_SmaI) == 2686 )
self.assertTrue( pUC19_SmaI.linear )
pUC19_SmaI_a = pUC19_SmaI.seq + a
self.assertTrue( pUC19_SmaI_a.linear )
self.assertFalse( pUC19_SmaI_a.circular )
pUC19_SmaI_a=pUC19_SmaI_a.looped()
self.assertTrue( len(pUC19_SmaI_a) == 2778 )
self.assertTrue( pUC19_SmaI_a.circular )
self.assertFalse( pUC19_SmaI_a.linear )
self.assertTrue( eq(pUC19_SmaI_a, read("./pUC19-SmaI-a.gb") ))
''' sticky end cloning '''
pUC19_BamHI = pUC19.cut(BamHI)
self.assertTrue( len(pUC19_BamHI) == 1)
pUC19_BamHI = pUC19_BamHI.pop().seq
self.assertTrue( len(pUC19_BamHI.watson) == len(pUC19_BamHI.crick) == 2686 )
pUC19_BamHI_a = pUC19_BamHI+b
self.assertTrue( len(pUC19_BamHI_a.watson) == len(pUC19_BamHI_a.crick) == 2772 )
self.assertTrue( pUC19_BamHI_a.circular == False)
self.assertTrue( pUC19_BamHI_a.linear == True)
pUC19_BamHI_a = pUC19_BamHI_a.looped()
self.assertTrue( pUC19_BamHI_a.circular == True)
self.assertTrue( pUC19_BamHI_a.linear == False)
self.assertTrue( eq(pUC19_BamHI_a, read("./pUC19-BamHI-a.gb")))
pUC19_BamHI_a_rc = pUC19_BamHI+b.rc()
pUC19_BamHI_a_rc = pUC19_BamHI_a_rc.looped()
self.assertTrue( pUC19_BamHI_a.circular == True)
self.assertTrue( pUC19_BamHI_a.linear == False)
self.assertTrue( eq(pUC19_BamHI_a_rc, read("./pUC19-BamHI-a-rc.gb")))
''' adding (ligating) dsDNA objects '''
with self.assertRaisesRegexp(TypeError, "circular"):
pUC19+a
with self.assertRaisesRegexp(TypeError, "circular"):
a+pUC19
with self.assertRaisesRegexp(TypeError, "compatible"):
a+b
with self.assertRaisesRegexp(TypeError, "compatible"):
b+a
with self.assertRaisesRegexp(TypeError, "compatible"):
d+d
''' directional cloning '''
pUC19_EcoRI_PstI = pUC19.cut(EcoRI, PstI).pop(0)
with self.assertRaisesRegexp(TypeError, "compatible"):
pUC19_EcoRI_PstI + d
pUC19_EcoRI_PstI_d = pUC19_EcoRI_PstI + d.rc()
pUC19_EcoRI_PstI_d = pUC19_EcoRI_PstI_d.looped()
self.assertTrue( eq(pUC19_EcoRI_PstI_d, read("./pUC19-EcoRI_PstI-d-rc.gb")))
self.assertTrue( eq(pUC19_EcoRI_PstI_d.rc(), read("./pUC19-EcoRI_PstI-d-rc.gb")))
def test_Dseq_cutting_adding(self):
from Bio.Seq import Seq
from Bio.Restriction import BamHI, EcoRI, PstI, EcoRV, SmaI
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio.SeqUtils.CheckSum import seguid
from pydna import Dseq
a = Dseq(
'GGATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGGATCC',
'CCTAGGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCCTAGG'[::
-1],
linear=True,
ovhg=0)
b = a.cut(BamHI)[1]
self.assertEqual(
b.watson,
"GATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG"
)
self.assertEqual(
b.crick,
"GATCCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG"
)
c = Dseq(
'nCTGCAGtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGAATTCn',
'nGACGTCagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaCTTAAGn'[::
-1],
linear=True,
ovhg=0)
f, d, l = c.cut((EcoRI, PstI))
self.assertEqual(
d.watson,
"GtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG"
)
self.assertEqual(
d.crick,
"AATTCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaCTGCA"
)
e = Dseq(
"nGAATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCAGn",
"nCTTAAGagtagatgatagtagcatcgcatgactagataagacgacgagtagtagccatgagagatattaatatatatatacgcgcaGACGTCn"[::
-1],
linear=True,
ovhg=0)
f = e.cut((EcoRI, PstI))[1]
self.assertEqual(
f.watson,
"AATTCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtCTGCA"
)
self.assertEqual(
f.crick,
"GacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaG"
)
''' blunt cloning '''
pUC19 = read("./pUC19.gb")
self.assertFalse(pUC19.linear)
self.assertTrue(len(pUC19) == 2686)
self.assertTrue(len(pUC19.seq.watson) == 2686)
self.assertTrue(len(pUC19.seq.crick) == 2686)
self.assertTrue(pUC19.seq.circular == True)
self.assertTrue(pUC19.seq.linear == False)
pUC19_SmaI = pUC19.cut(SmaI)
self.assertTrue(len(pUC19_SmaI) == 1)
pUC19_SmaI = pUC19_SmaI.pop()
self.assertTrue(pUC19_SmaI.linear)
self.assertTrue(len(pUC19_SmaI) == 2686)
self.assertTrue(pUC19_SmaI.linear)
pUC19_SmaI_a = pUC19_SmaI.seq + a
self.assertTrue(pUC19_SmaI_a.linear)
self.assertFalse(pUC19_SmaI_a.circular)
pUC19_SmaI_a = pUC19_SmaI_a.looped()
self.assertTrue(len(pUC19_SmaI_a) == 2778)
self.assertTrue(pUC19_SmaI_a.circular)
self.assertFalse(pUC19_SmaI_a.linear)
self.assertTrue(eq(pUC19_SmaI_a, read("./pUC19-SmaI-a.gb")))
''' sticky end cloning '''
pUC19_BamHI = pUC19.cut(BamHI)
self.assertTrue(len(pUC19_BamHI) == 1)
pUC19_BamHI = pUC19_BamHI.pop().seq
self.assertTrue(
len(pUC19_BamHI.watson) == len(pUC19_BamHI.crick) == 2686)
pUC19_BamHI_a = pUC19_BamHI + b
self.assertTrue(
len(pUC19_BamHI_a.watson) == len(pUC19_BamHI_a.crick) == 2772)
self.assertTrue(pUC19_BamHI_a.circular == False)
self.assertTrue(pUC19_BamHI_a.linear == True)
pUC19_BamHI_a = pUC19_BamHI_a.looped()
self.assertTrue(pUC19_BamHI_a.circular == True)
self.assertTrue(pUC19_BamHI_a.linear == False)
self.assertTrue(eq(pUC19_BamHI_a, read("./pUC19-BamHI-a.gb")))
pUC19_BamHI_a_rc = pUC19_BamHI + b.rc()
pUC19_BamHI_a_rc = pUC19_BamHI_a_rc.looped()
self.assertTrue(pUC19_BamHI_a.circular == True)
self.assertTrue(pUC19_BamHI_a.linear == False)
self.assertTrue(eq(pUC19_BamHI_a_rc, read("./pUC19-BamHI-a-rc.gb")))
''' adding (ligating) dsDNA objects '''
with self.assertRaisesRegexp(TypeError, "circular"):
pUC19 + a
with self.assertRaisesRegexp(TypeError, "circular"):
a + pUC19
with self.assertRaisesRegexp(TypeError, "compatible"):
a + b
with self.assertRaisesRegexp(TypeError, "compatible"):
b + a
with self.assertRaisesRegexp(TypeError, "compatible"):
d + d
''' directional cloning '''
pUC19_EcoRI_PstI = pUC19.cut(EcoRI, PstI).pop(0)
with self.assertRaisesRegexp(TypeError, "compatible"):
pUC19_EcoRI_PstI + d
pUC19_EcoRI_PstI_d = pUC19_EcoRI_PstI + d.rc()
pUC19_EcoRI_PstI_d = pUC19_EcoRI_PstI_d.looped()
self.assertTrue(
eq(pUC19_EcoRI_PstI_d, read("./pUC19-EcoRI_PstI-d-rc.gb")))
self.assertTrue(
eq(pUC19_EcoRI_PstI_d.rc(), read("./pUC19-EcoRI_PstI-d-rc.gb")))
