def test_shift_origin(self):
pCAPs = read("./pCAPs.gb")
self.assertTrue( pCAPs.circular )
pCAPs_b = shift_origin(pCAPs, 200)
self.assertEqual( len(pCAPs), len(pCAPs_b) )
self.assertTrue( pCAPs_b.circular )
self.assertTrue( eq(pCAPs, pCAPs_b) )
pCAPs_b_linear = pCAPs_b.tolinear()
self.assertTrue( eq(pCAPs, pCAPs_b_linear, circular=True) )
pCAPs_c = pCAPs[200:]+pCAPs[:200]
self.assertTrue( eq(pCAPs, pCAPs_c, circular=True) )
with self.assertRaisesRegexp(ValueError, "shift"):
pCAPs_b = shift_origin(pCAPs, 20000)
def test_shift_origin(self):
pCAPs = read("./pCAPs.gb")
self.assertTrue(pCAPs.circular)
pCAPs_b = shift_origin(pCAPs, 200)
self.assertEqual(len(pCAPs), len(pCAPs_b))
self.assertTrue(pCAPs_b.circular)
self.assertTrue(eq(pCAPs, pCAPs_b))
pCAPs_b_linear = pCAPs_b.tolinear()
self.assertTrue(eq(pCAPs, pCAPs_b_linear, circular=True))
pCAPs_c = pCAPs[200:] + pCAPs[:200]
self.assertTrue(eq(pCAPs, pCAPs_c, circular=True))
with self.assertRaisesRegexp(ValueError, "shift"):
pCAPs_b = shift_origin(pCAPs, 20000)
def test_empty(self):
""" test YEp24PGK_XK"""
import os
import pydna
cwd = os.getcwd()
YEp24PGK_XK_correct = pydna.read("YEp24PGK_XK_correct.gb")
os.chdir("../docs/cookbook/")
p1 = pydna.read("primer1.txt", ds=False)
p3 = pydna.read("primer3.txt", ds=False)
XKS1 = pydna.read("XKS1_orf.txt")
YEp24PGK = pydna.read("YEp24PGK.txt")
os.chdir(cwd)
PCR_prod = pydna.pcr(p1, p3, XKS1)
from Bio.Restriction import BamHI
stuffer1, insert, stuffer2 = PCR_prod.cut(BamHI)
from Bio.Restriction import BglII
YEp24PGK_BglII = YEp24PGK.cut(BglII).pop()
YEp24PGK_XK = YEp24PGK_BglII + insert
YEp24PGK_XK = YEp24PGK_XK.looped()
YEp24PGK_XK = YEp24PGK_XK.synced("gaattctgaaccagtcctaaaacgagtaaataggaccggcaattc") # YEp24PGK)
self.assertTrue(pydna.eq(YEp24PGK_XK, YEp24PGK_XK_correct))
self.assertEqual(YEp24PGK_XK_correct.seguid(), "HRVpCEKWcFsKhw_W-25ednUfldI")
self.assertEqual(YEp24PGK_XK.seguid(), "HRVpCEKWcFsKhw_W-25ednUfldI")
def test_empty(self):
''' test YEp24PGK_XK'''
import os
import pydna
cwd = os.getcwd()
YEp24PGK_XK_correct = pydna.read("YEp24PGK_XK_correct.gb")
os.chdir("../docs/cookbook/")
p1 = pydna.read("primer1.txt", ds = False)
p3 = pydna.read("primer3.txt", ds = False)
XKS1 = pydna.read("XKS1_orf.txt")
YEp24PGK = pydna.read("YEp24PGK.txt")
os.chdir(cwd)
PCR_prod = pydna.pcr(p1, p3, XKS1)
from Bio.Restriction import BamHI
stuffer1, insert, stuffer2 = PCR_prod.cut(BamHI)
from Bio.Restriction import BglII
YEp24PGK_BglII = YEp24PGK.cut(BglII).pop()
YEp24PGK_XK = YEp24PGK_BglII + insert
YEp24PGK_XK=YEp24PGK_XK.looped()
YEp24PGK_XK = YEp24PGK_XK.synced("gaattctgaaccagtcctaaaacgagtaaataggaccggcaattc") #YEp24PGK)
self.assertTrue( pydna.eq(YEp24PGK_XK, YEp24PGK_XK_correct))
self.assertEqual( YEp24PGK_XK_correct.seguid() ,"HRVpCEKWcFsKhw_W-25ednUfldI" )
self.assertEqual( YEp24PGK_XK.seguid() ,"HRVpCEKWcFsKhw_W-25ednUfldI" )
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_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_empty(self):
''' test pGUP1'''
import os
cwd = os.getcwd()
os.chdir("../docs/cookbook/")
import pydna
GUP1rec1sens = pydna.read("GUP1rec1sens.txt")
GUP1rec2AS = pydna.read("GUP1rec2AS.txt")
GUP1_locus = pydna.read("GUP1_locus.gb")
pGREG505 = pydna.read("pGREG505.gb")
os.chdir(cwd)
insert = pydna.pcr(GUP1rec1sens, GUP1rec2AS, GUP1_locus)
from Bio.Restriction import SalI
lin_vect, his3 = pGREG505.cut(SalI)
a = pydna.Assembly([insert, lin_vect], limit=28)
pGUP1 = a.circular_products[0]
pGUP1 = pGUP1.synced(pGREG505.seq[:50])
pGUP1_correct = pydna.read("pGUP1_correct.gb")
self.assertEqual(len(pGUP1_correct), 9981)
self.assertEqual(len(pGUP1), 9981)
self.assertTrue(pydna.eq(pGUP1, pGUP1_correct))
self.assertEqual(pGUP1_correct.seguid(), "42wIByERn2kSe_Exn405RYwhffU")
self.assertEqual(pGUP1.seguid(), "42wIByERn2kSe_Exn405RYwhffU")
from pydna import parse, eq
new_primer = parse("/home/bjorn/Dropbox/wikidata/PrimersToBuy.wiki", ds=False)
primer = parse("/home/bjorn/Dropbox/wikidata/Primers.wiki", ds=False)
primer = primer[::-1]
old_primer = primer[:37 + 18]
primer = primer[37 + 18:]
new_primer_dict = dict((p.id, p) for p in new_primer)
primer_dict = dict((p.id, p) for p in primer)
old_primer_dict = dict((p.id, p) for p in old_primer)
assert str(primer_dict["509_mycGFPr"].seq) == "CTACTTGTACAGCTCGTCCA"
assert primer[0].id == "0_S1"
assert primer[1].id == "1_5CYC1clone"
assert primer[580].id == "580_GXF1_YPK_fwd"
fprimer = parse("/home/bjorn/Dropbox/wikidata/New10.wiki", ds=False)
fprimer = fprimer[::-1]
fold_primer = fprimer[:37 + 18]
fprimer = fprimer[37 + 18:]
print len(primer), len(fprimer)
for i in range(1, len(primer)):
if not eq(primer[i], fprimer[i]):
print i
print primer[i].id, fprimer[i].id
raw_input()
def test_features_change_ori(self):
s = read('''
LOCUS New_DNA 13 bp ds-DNA circular 12-NOV-2013
DEFINITION .
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature join(9..10,12..13,1..1,3..6)
/label=hej
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
ORIGIN
1 gattttaatc acc
//''')
#from pydna_helper import ape
for i in range(1, len(s)):
b = s.shifted(i)
self.assertTrue(
str(b.features[0].extract(b).seq).lower() == "tcccgtttt")
s = read('''
LOCUS New_DNA 21 bp ds-DNA circular 03-APR-2013
DEFINITION a
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature join(18..21,1..4)
/label=bb
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 5..17
/label=ins
/ApEinfo_fwdcolor=#e03c2b
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
ORIGIN
1 aaaGGTACCt ttGGATCCggg
//
''')
self.assertTrue(str(s.features[0].extract(s).seq) == "CGGGAAAG")
self.assertTrue(str(s.features[1].extract(s).seq) == "GTACCTTTGGATC")
for i in range(1, len(s)):
b = s.shifted(i)
self.assertTrue([
str(f.extract(b).seq) for f in b.features
if f.qualifiers["label"][0] == 'ins'
][0] == "GTACCTTTGGATC")
self.assertTrue([
str(f.extract(b).seq) for f in b.features
if f.qualifiers["label"][0] == 'bb'
][0] == "CGGGAAAG")
from Bio.Restriction import Acc65I, KpnI, BamHI
bb1, ins1 = sorted(s.cut(Acc65I, BamHI), key=len, reverse=True)
for i in range(1, len(s)):
b = s.shifted(i)
bb, ins = sorted(b.cut(Acc65I, BamHI), key=len, reverse=True)
self.assertTrue(eq(bb1, bb))
self.assertTrue(eq(ins1, ins))
self.assertTrue(
bb.features[0].extract(bb).seq.watson == "CGGGAAAG")
self.assertTrue(bb.features[0].extract(bb).seq.crick == "CTTTCCCG")
self.assertTrue(
eq(bb.features[0].extract(bb), s.features[0].extract(s)))
self.assertTrue(
ins.features[0].extract(ins).seq.watson == "GTACCTTTG")
self.assertTrue(
ins.features[0].extract(ins).seq.crick == "GATCCAAAG")
self.assertTrue(
str(ins.features[0].extract(ins).seq) == str(
s.features[1].extract(s).seq))
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
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 21..33
/label=NlaIV-3
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
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")))
def test_eq(self):
''' test eq'''
self.assertTrue(eq("AAA", "TTT", linear=True))
self.assertTrue(eq("AAA", "TTT", linear=False))
self.assertTrue(eq("aAA", "TtT", linear=True))
self.assertTrue(eq("AAa", "TtT", linear=False))
self.assertTrue(eq("ATA", "AAT", circular=True))
self.assertFalse(eq("ATA", "AAT", circular=False))
self.assertTrue(eq("AAA", "AAA", linear=True))
self.assertTrue(eq("AAA", "AAA", linear=False))
self.assertTrue(eq("ATA", Seq("AAT"), circular=True))
self.assertFalse(eq("ATA", Seq("AAT"), circular=False))
self.assertTrue(eq("AAA", Seq("AAA"), linear=True))
self.assertTrue(eq("AAA", Seq("AAA"), linear=False))
self.assertTrue(eq("ATA", SeqRecord("AAT"), circular=True))
self.assertFalse(eq("ATA", SeqRecord("AAT"), circular=False))
self.assertTrue(eq("AAA", SeqRecord("AAA"), linear=True))
self.assertTrue(eq("AAA", SeqRecord("AAA"), linear=False))
self.assertTrue(eq("ATA", Dseqrecord("AAT"), circular=True))
self.assertFalse(eq("ATA", Dseqrecord("AAT"), circular=False))
self.assertTrue(eq("AAA", Dseqrecord("AAA"), linear=True))
self.assertTrue(eq("AAA", Dseqrecord("AAA"), linear=False))
self.assertTrue(eq(Seq("ATA"), SeqRecord("AAT"), circular=True))
self.assertFalse(eq(Seq("ATA"), SeqRecord("AAT"), circular=False))
self.assertTrue(eq(Seq("AAA"), SeqRecord("AAA"), linear=True))
self.assertTrue(eq(Seq("AAA"), SeqRecord("AAA"), linear=False))
self.assertTrue(eq(Seq("ATA"), Dseqrecord("AAT"), circular=True))
self.assertFalse(eq(Seq("ATA"), Dseqrecord("AAT"), circular=False))
self.assertTrue(eq(Seq("AAA"), Dseqrecord("AAA"), linear=True))
self.assertTrue(eq(Seq("AAA"), Dseqrecord("AAA"), linear=False))
self.assertTrue(
eq(Dseqrecord("AAA", circular=False),
Dseqrecord("AAA", circular=False)))
self.assertTrue(
eq(Dseqrecord("AAA", circular=True),
Dseqrecord("AAA", circular=True)))
self.assertFalse(
eq(Dseqrecord("ATA", circular=False),
Dseqrecord("AAT", circular=False)))
self.assertTrue(
eq(Dseqrecord("ATA", circular=True),
Dseqrecord("AAT", circular=True)))
self.assertEqual(True, True)
self.assertTrue(True)
self.assertFalse(False)
with self.assertRaises(TypeError):
1 + "1"
with self.assertRaisesRegexp(TypeError, "unsupported"):
1 + "1"