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_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_rogerstager(self):
from Bio.Seq import Seq
from Bio.Restriction import BsaI
answ = []
answ.append(Dseq('aaaaaaaaaaaaggtctca', 'ttttttttccagagttttt'[::-1]))
answ.append(Dseq('aaaaaaaaaggtctca', 'tttttccagagttttt'[::-1]))
tests = [Seq("aaaaaaggtctcaaaaaaa"), Seq("aaaaaaggtctcaaaa")]
for s in tests:
d = Dseqrecord(s).looped()
for f in d.cut(BsaI):
a = answ.pop(0)
self.assertTrue(f.seq.watson == a.watson)
self.assertTrue(f.seq.crick == a.crick)
self.assertTrue(f.seq.ovhg == a.ovhg)
self.assertTrue(eq(f.seq, a))
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_map(self):
traces = []
import glob
for name in glob.glob('*.ab1'):
traces.append(abiread(name, "abi"))
for t in traces:
d = Dseqrecord(t.seq)
if "ITVFFKEYPYDVPDYAIEGIFHAT" in d:
tag = "tat cca tat gac gtt cca gac tat gca"
trc = "ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s)
tag = "AAA tat cca tat gac gtt cca gac tat gca"
trc = " ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s)
tag = " tat cca tat gac gtt cca gac tat gca"
trc = "AAA ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s)
tag = " tat cca tat gac gtt cca gac tat gca"
trc = "AAA ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
tag = "tat cca tat gac gtt cca gac tat gca"
trc = "ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
tag, trc = trc, tag
s = Dseqrecord(Dseq(tag, trc))
sl = s.rc().find_aa("YPYDVPDYA")
self.assertTrue(str(s.rc()[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s.rc())
tag = "aaa tat cca tat gac gtt cca gac tat gca"
trc = "ttt ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc, circular=True))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s)
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_initialization(self):
a = []
a.append(Dseqrecord("attt"))
a.append(Dseqrecord(Dseq("attt")))
a.append(Dseqrecord(Seq("attt")))
a.append(Dseqrecord(Srec(Seq("attt"))))
a.append(Dseqrecord(Dseqrecord("attt")))
for b in a:
self.assertTrue(type(b.seq) == Dseq)
self.assertTrue(str(b.seq.watson) == "attt")
self.assertTrue(str(b.seq.crick) == "aaat")
self.assertTrue(str(b.seq) == "attt")
self.assertTrue(str(b.seq) == "attt")
self.assertTrue(b.linear == b.seq.linear)
self.assertTrue(b.linear == True)
self.assertTrue(b.circular == False)
self.assertTrue(b.seq.linear == True)
self.assertTrue(b.seq.circular == False)
a = []
a.append(Dseqrecord("attt", circular=True))
a.append(Dseqrecord(Dseq("attt"), circular=True))
a.append(Dseqrecord(Seq("attt"), circular=True))
a.append(Dseqrecord(Srec(Seq("attt")), circular=True))
a.append(Dseqrecord(Dseqrecord("attt"), circular=True))
for b in a:
self.assertTrue(type(b.seq) == Dseq)
self.assertTrue(str(b.seq.watson) == "attt")
self.assertTrue(str(b.seq.crick) == "aaat")
self.assertTrue(str(b.seq) == "attt")
self.assertTrue(str(b.seq) == "attt")
self.assertTrue(b.linear == b.seq.linear)
self.assertTrue(b.linear == False)
self.assertTrue(b.circular == True)
self.assertTrue(b.seq.linear == False)
self.assertTrue(b.seq.circular == True)
a = []
a.append(Dseqrecord(Dseq("attt", circular=True), circular=True))
a.append(Dseqrecord(Dseq("attt", circular=False), circular=True))
a.append(Dseqrecord(Dseq("attt", circular=True), circular=False))
a.append(Dseqrecord(Dseq("attt", circular=False), circular=False))
circular = [True, True, False, False]
linear = [False, False, True, True]
for b, ci, li in zip(a, circular, linear):
self.assertTrue(type(b.seq) == Dseq)
self.assertTrue(str(b.seq.watson) == "attt")
self.assertTrue(str(b.seq.crick) == "aaat")
self.assertTrue(str(b.seq) == "attt")
self.assertTrue(str(b.seq) == "attt")
self.assertTrue(b.linear == b.seq.linear)
self.assertTrue(b.linear == li)
self.assertTrue(b.circular == ci)
self.assertTrue(b.seq.linear == li)
self.assertTrue(b.seq.circular == ci)
a = []
ds = Dseq("attt", "taaa")
self.assertTrue(ds.linear == True)
self.assertTrue(ds.ovhg == -1)
self.assertTrue(str(ds.watson) == "attt")
self.assertTrue(str(ds.crick) == "taaa")
# attt
# aaat
a.append(Dseqrecord(ds, circular=False))
self.assertTrue(ds.linear == True)
a.append(Dseqrecord(ds, linear=True))
self.assertTrue(ds.linear == True)
a.append(Dseqrecord(ds, circular=True))
self.assertTrue(ds.linear == True)
a.append(Dseqrecord(ds, linear=False))
self.assertTrue(ds.linear == True)
circular = [False, False, True, True]
linear = [True, True, False, False]
crick = ["taaa", "taaa", "aaat", "aaat"]
sek = ["attta", "attta", "attt", "attt"]
for b, ci, li, s, cri in zip(a, circular, linear, sek, crick):
self.assertTrue(type(b.seq) == Dseq)
self.assertTrue(str(b.seq.watson) == "attt")
self.assertTrue(str(b.seq.crick) == cri)
self.assertTrue(str(b.seq) == s)
self.assertTrue(b.linear == b.seq.linear)
self.assertTrue(b.linear == li)
self.assertTrue(b.circular == ci)
self.assertTrue(b.seq.linear == li)
self.assertTrue(b.seq.circular == ci)
a = []
ds = Dseq("attt", "caaa")
self.assertTrue(ds.linear == True)
self.assertTrue(ds.ovhg == -1)
a.append(Dseqrecord(ds, circular=False))
self.assertTrue(ds.linear == True)
a.append(Dseqrecord(ds, linear=True))
self.assertTrue(ds.linear == True)
with self.assertRaises(TypeError):
Dseqrecord(ds, circular=True)
self.assertTrue(ds.linear == True)
with self.assertRaises(TypeError):
Dseqrecord(ds, linear=False)
self.assertTrue(ds.linear == True)
with self.assertRaises(TypeError):
b = Dseqrecord([])
with self.assertRaises(TypeError):
b = Dseqrecord(("a", ))
with self.assertRaises(TypeError):
b = Dseqrecord(0)
from pydna import read
input = '''
LOCUS New_DNA 4 bp ds-DNA linear 30-MAR-2013
DEFINITION .
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 2..3
/label=NewFeature
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
ORIGIN
1 acgt
//
'''
a = read(input)
self.assertEqual(a.features[0].extract(a).seq.watson, "CG")
b = a + a
for f in b.features:
self.assertEqual(b.features[0].extract(a).seq.watson, "CG")
feature = a.features[0]
s = Dseq("agctt", "agcta")
#print s.fig()
#Dseq(-6)
# agctt
#atcga
b = Dseqrecord(s)
b.features.append(feature)
cb = Dseqrecord(b, circular=True)
self.assertEqual(b.features[0].extract(b).seq.watson.lower(),
cb.features[0].extract(b).seq.watson.lower())
self.assertEqual(b.features[0].extract(b).seq.crick.lower(),
cb.features[0].extract(b).seq.crick.lower())
s = Dseq("aagct", "aagct")
#print s.fig()
#Dseq(-6)
#aagct
# tcgaa
b = Dseqrecord(s)
with self.assertRaises(TypeError):
cb = Dseqrecord(b, circular=True)
s = Dseq("agctt", "agcta")
#print s.fig()
#Dseq(-6)
# agcta
#ttcga
b = Dseqrecord(s)
b.features.append(feature)
cb = Dseqrecord(b, circular=True)
self.assertEqual(b.features[0].extract(b).seq.watson.lower(),
cb.features[0].extract(b).seq.watson.lower())
self.assertEqual(b.features[0].extract(b).seq.crick.lower(),
cb.features[0].extract(b).seq.crick.lower())
def test_Dseqrecord_cutting_adding(self):
from Bio.Restriction import Bsu36I, BstAPI
pCAPs = read("./pCAPs.gb")
a, b = pCAPs.cut(Bsu36I, BstAPI)
c = (a + b).looped()
self.assertTrue(eq(c, pCAPs))
a = (
Dseqrecord(
Dseq('AATTCACANGGTACCNGGTACCNGCGGATATC',
'GTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], -4)),
Dseqrecord(
Dseq('CACANGGTACCNGGTACCNGCGGATATC',
'GTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], 0)),
Dseqrecord(
Dseq('CACANGGTACCNGGTACCNGCGGATATC',
'AATTGTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], 4)),
)
from Bio.Restriction import KpnI, Acc65I, NlaIV
enzymes = [Acc65I, NlaIV, KpnI]
for enz in enzymes:
for f in a:
b, c, d = f.cut(enz)
e = b + c + d
assert str(e.seq).lower() == str(f.seq).lower()
#from pydna import *
#from pydna_helper import gb, ape
from Bio.Restriction import KpnI, BamHI, Acc65I, NlaIV, EcoRI, EcoRV
a = read('''
LOCUS New_DNA 10 bp ds-DNA linear 02-APR-2013
DEFINITION
ACCESSION New_DNA
VERSION New_DNA
KEYWORDS .
SOURCE
ORGANISM . .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 1..1
/label=1
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 2..2
/label=2
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 3..3
/label=3
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 4..4
/label=4
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 5..5
/label=5
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 6..6
/label=6
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 7..7
/label=7
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 8..8
/label=8
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 9..9
/label=9
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 10..10
/label=10
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
ORIGIN
1 ttGGTACCgg
//''')
b, c = a.cut(Acc65I)
self.assertEqual([f.qualifiers["label"] for f in b.features],
[['1'], ['2'], ['3'], ['4'], ['5'], ['6'], ['7']])
self.assertEqual([f.qualifiers["label"] for f in c.features],
[['4'], ['5'], ['6'], ['7'], ['8'], ['9'], ['10']])
a = read('''
LOCUS New_DNA 33 bp ds-DNA linear 08-NOV-2012
DEFINITION .
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 1..11
/label=Acc65I-1
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 12..18
/label=Acc65I-2
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 19..33
/label=Acc65I-3
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 1..15
/label=KpnI-1
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 16..22
/label=KpnI-2
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 23..33
/label=KpnI-3
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 1..13
/label=NlaIV-1
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 14..20
/label=NlaIV-2
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misc_feature 21..33
/label=NlaIV-3
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
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ORIGIN
1 GAATTCacan ggtaccnGGT ACCngcgGAT ATC
//
''')
self.assertTrue(a.seguid() == "di3hL8t2G4iQQsxlm_CtvnUMBz8")
self.assertTrue(([x.qualifiers["label"][0] for x in a.features] == [
'Acc65I-1', 'Acc65I-2', 'Acc65I-3', 'KpnI-1', 'KpnI-2', 'KpnI-3',
'NlaIV-1', 'NlaIV-2', 'NlaIV-3'
]))
b, c, d = a.cut(Acc65I)
self.assertTrue(
[x.qualifiers["label"][0]
for x in b.features] == ['Acc65I-1', 'KpnI-1', 'NlaIV-1'])
self.assertTrue(
[x.qualifiers["label"][0]
for x in c.features] == ['Acc65I-2', 'KpnI-2', 'NlaIV-2'])
self.assertTrue(
[x.qualifiers["label"][0]
for x in d.features] == ['Acc65I-3', 'KpnI-3', 'NlaIV-3'])
e = b + c + d
self.assertTrue(
sorted([x.qualifiers["label"][0] for x in e.features]) ==
[x.qualifiers["label"][0] for x in a.features])
self.assertTrue(str(a.seq) == str(e.seq))
b, c, d = a.cut(KpnI)
self.assertTrue(
[x.qualifiers["label"][0]
for x in b.features] == ['Acc65I-1', 'KpnI-1', 'NlaIV-1'])
self.assertTrue(
[x.qualifiers["label"][0]
for x in c.features] == ['Acc65I-2', 'KpnI-2', 'NlaIV-2'])
self.assertTrue(
[x.qualifiers["label"][0]
for x in d.features] == ['Acc65I-3', 'KpnI-3', 'NlaIV-3'])
e = b + c + d
self.assertTrue(
sorted([x.qualifiers["label"][0] for x in e.features]) ==
[x.qualifiers["label"][0] for x in a.features])
b, c, d = a.cut(NlaIV)
self.assertTrue([x.qualifiers["label"][0]
for x in b.features] == ['Acc65I-1', 'NlaIV-1'])
self.assertTrue([x.qualifiers["label"][0]
for x in c.features] == ['NlaIV-2'])
self.assertTrue([x.qualifiers["label"][0]
for x in d.features] == ['KpnI-3', 'NlaIV-3'])
e = b + c + d
self.assertTrue(str(a.seq) == str(e.seq))
b, c = a.cut(EcoRI)
e = b + c
self.assertTrue(str(a.seq) == str(e.seq))
b, c = a.cut(EcoRV)
e = b + c
self.assertTrue(str(a.seq) == str(e.seq))
b, c, d = a.cut(EcoRI, EcoRV)
e = b + c + d
self.assertTrue(str(a.seq) == str(e.seq))
b, c, d, f = a.cut(Acc65I, EcoRI)
e = b + c + d + f
self.assertTrue(str(a.seq) == str(e.seq))
b, c, d, f = a.cut(EcoRI, Acc65I)
e = b + c + d + f
self.assertTrue(str(a.seq) == str(e.seq))
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")))