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 test_synced3(self):
pGUP1 = read("pGUP1_correct.gb")
pGREG505 = read("pGREG505.gb")
pGUP1_not_synced = read("pGUP1_not_synced.gb")
self.assertEqual(
pGUP1_not_synced.synced(pGREG505).seguid(),
'42wIByERn2kSe_Exn405RYwhffU')
def test_read_from_file():
a = read("./read1.gb")
b = read("./read2.gb")
c = read("./read3.fasta")
d = read("./read4.fasta")
a.format("gb")
b.format("gb")
c.format("gb")
d.format("gb")
assert str(a.seq).lower()==str(b.seq).lower()==str(c.seq).lower()==str(d.seq).lower()
def test_synced2(self):
pUC19 = read("./pUC19.gb")
pUC19_small_gene = read("./pUC19_small_gene.gb")
correct = str(pUC19_small_gene.seq).upper()
for i in range(1, len(pUC19_small_gene), 500):
cand = pUC19_small_gene.shifted(i)
self.assertEqual(str(cand.synced("tcgcgcgtttcggtgatgacggtga").seq).upper(),
correct,
str(cand.synced(pUC19).seq).upper())
print i,
print
def test_synced2(self):
pUC19 = read("./pUC19.gb")
pUC19_small_gene = read("./pUC19_small_gene.gb")
correct = str(pUC19_small_gene.seq).upper()
for i in range(1, len(pUC19_small_gene), 500):
cand = pUC19_small_gene.shifted(i)
self.assertEqual(
str(cand.synced("tcgcgcgtttcggtgatgacggtga").seq).upper(),
correct,
str(cand.synced(pUC19).seq).upper())
print i,
print
def test_synced(self):
pUC19 = read("./pUC19.gb")
pUC19_LAC4 = read("./pUC_LAC4.gb")
pUC19_LAC4_c = read("pUC_LAC4_correct_rotation.gb")
correct = str(pUC19_LAC4_c.seq).upper()
for i in range(1, len(pUC19_LAC4), 500):
cand = pUC19_LAC4.shifted(i)
self.assertEqual(str(cand.synced("tcgcgcgtttcggtgatgacggtga").seq).upper(),
correct,
str(pUC19_LAC4.synced(pUC19).seq).upper())
print i,
print
def test_synced(self):
pUC19 = read("./pUC19.gb")
pUC19_LAC4 = read("./pUC_LAC4.gb")
pUC19_LAC4_c = read("pUC_LAC4_correct_rotation.gb")
correct = str(pUC19_LAC4_c.seq).upper()
for i in range(1, len(pUC19_LAC4), 500):
cand = pUC19_LAC4.shifted(i)
self.assertEqual(
str(cand.synced("tcgcgcgtttcggtgatgacggtga").seq).upper(),
correct,
str(pUC19_LAC4.synced(pUC19).seq).upper())
print i,
print
def test_read_from_file():
a = read("./read1.gb")
b = read("./read2.gb")
c = read("./read3.fasta")
d = read("./read4.fasta")
x,y = parse( "pth1.txt" )
a.format("gb")
b.format("gb")
c.format("gb")
d.format("gb")
x.format("gb")
y.format("gb")
assert x.format()[3314:3325] == '2micron 2\xc2\xb5'
assert x.features[13].qualifiers['label'][0] == '2micron 2\xc2\xb5'
assert str(a.seq).lower()==str(b.seq).lower()==str(c.seq).lower()==str(d.seq).lower()
def test_map2(self):
pCR_MCT1_HA46 = read("pCR_MCT1_HA46.gb")
slc = pCR_MCT1_HA46.find_aa("VFFKE YPYDVPDYA IEG".replace(" ", ""))
pCR_MCT1_HA46.map_target = slc
map_ = pCR_MCT1_HA46.map_trace_files("*.ab1")
self.assertTrue(
set(map_) == set([
'28-1rev_D04_026.ab1', '32-3rev_H04_018.ab1',
'36-5rev_D05_041.ab1'
]))
self.assertTrue(
set([x.fname for x in pCR_MCT1_HA46.matching_reads]) == set([
'28-1rev_D04_026.ab1', '32-3rev_H04_018.ab1',
'36-5rev_D05_041.ab1'
]))
self.assertTrue(
set([x.fname for x in pCR_MCT1_HA46.not_matching_reads]) == set(
['02-G1_B01_013.ab1']))
self.assertTrue(
pCR_MCT1_HA46.find_aa("YPYDVPDYA".replace(" ", "")) == slice(
1088, 1115, None))
self.assertTrue(
pCR_MCT1_HA46.find_aa("VFFKE YPYDVPDYA IEG".replace(" ", "")) ==
slice(1073, 1124, None))
def test_read_from_file():
a = read("./read1.gb")
b = read("./read2.gb")
c = read("./read3.fasta")
d = read("./read4.fasta")
x, y = parse("pth1.txt")
a.format("gb")
b.format("gb")
c.format("gb")
d.format("gb")
x.format("gb")
y.format("gb")
assert x.format()[3314:3325] == '2micron 2\xc2\xb5'
assert x.features[13].qualifiers['label'][0] == '2micron 2\xc2\xb5'
assert str(a.seq).lower() == str(b.seq).lower() == str(
c.seq).lower() == str(d.seq).lower()
def test_empty(self):
''' test mark budde'''
import pydna
a = pydna.read('pGREG505.gb')
self.assertTrue(a.name, "pGREG505")
self.assertTrue(a.looped().name, "pGREG505")
#self.assertTrue( a.annotations ,"pGREG505")
self.assertTrue(a.id, "pGREG505")
self.assertTrue(a.looped().id, "pGREG505")
"""
def test_empty(self):
""" test mark budde"""
import pydna
a = pydna.read("pGREG505.gb")
self.assertTrue(a.name, "pGREG505")
self.assertTrue(a.looped().name, "pGREG505")
# self.assertTrue( a.annotations ,"pGREG505")
self.assertTrue(a.id, "pGREG505")
self.assertTrue(a.looped().id, "pGREG505")
"""
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 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")
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")
def test_cut_feat(self):
puc19 = read('PUC19_MarkBudde.gb')
pf, pr = cloning_primers(puc19)
pcrProd = pcr(pf, pr, puc19)
self.assertEqual(23, len(pcrProd.features))
#print len(pcrProd.cut(EcoRI)[1].features)
self.assertEqual(17, len(pcrProd.cut(EcoRI)[1].features))
def amplicon_to_dseqrecord(a):
d = Dseqrecord(a.seq)
d.features = a.features
return d
pcrProdDseqrecord = amplicon_to_dseqrecord(pcrProd)
self.assertEqual(17, len(pcrProdDseqrecord.cut(EcoRI)[1].features))
def test_cut_feat(self):
puc19 = read('PUC19_MarkBudde.gb')
pf, pr = cloning_primers(puc19)
pcrProd = pcr(pf, pr, puc19)
self.assertEqual(23, len(pcrProd.features))
#print len(pcrProd.cut(EcoRI)[1].features)
self.assertEqual(17, len(pcrProd.cut(EcoRI)[1].features))
def amplicon_to_dseqrecord(a):
d = Dseqrecord(a.seq)
d.features = a.features
return d
pcrProdDseqrecord = amplicon_to_dseqrecord(pcrProd)
self.assertEqual(17, len(pcrProdDseqrecord.cut(EcoRI)[1].features))
def ape(self, line):
import pydna
seq = ''
#print self.shell.user_ns[line]
try:
seq = self.shell.user_ns[line]
except KeyError:
pass
try:
seq = pydna.read(line)
except ValueError:
pass
if seq:
seq.description = line # new
MyMagics._apeloader.open(seq) #(*args,**kwargs)
return
def ape(self, line):
import pydna
seq=''
#print self.shell.user_ns[line]
try:
seq = self.shell.user_ns[line]
except KeyError:
pass
try:
seq = pydna.read(line)
except ValueError:
pass
if seq:
seq.description = line # new
MyMagics._apeloader.open(seq) #(*args,**kwargs)
return
def test_map2(self):
pCR_MCT1_HA46 = read("pCR_MCT1_HA46.gb")
slc = pCR_MCT1_HA46.find_aa("VFFKE YPYDVPDYA IEG".replace(" ", ""))
pCR_MCT1_HA46.map_target = slc
map_ = pCR_MCT1_HA46.map_trace_files("*.ab1")
self.assertTrue(set(map_)==set(['28-1rev_D04_026.ab1', '32-3rev_H04_018.ab1', '36-5rev_D05_041.ab1']))
self.assertTrue(set([x.fname for x in pCR_MCT1_HA46.matching_reads])==set(['28-1rev_D04_026.ab1', '32-3rev_H04_018.ab1', '36-5rev_D05_041.ab1']))
self.assertTrue(set([x.fname for x in pCR_MCT1_HA46.not_matching_reads])==set(['02-G1_B01_013.ab1']))
self.assertTrue(pCR_MCT1_HA46.find_aa("YPYDVPDYA".replace(" ", "")) == slice(1088, 1115, None))
self.assertTrue(pCR_MCT1_HA46.find_aa("VFFKE YPYDVPDYA IEG".replace(" ", "")) == slice(1073, 1124, None))
def test_read_from_string():
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_)
assert str(a.seq)=="ACGT"
input_ ='''>hej
acgt'''
assert str(a.seq)=="ACGT"
input_ =u'''
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_)
assert str(a.seq)=="ACGT"
input_ =u'''>hej
acgt'''
assert str(a.seq)=="ACGT"
input_ =u'''>hej öööh!
acgt'''
assert str(a.seq)=="ACGT"
input_ =u'''
LOCUS New_DNA 4 bp ds-DNA linear 30-MAR-2013
DEFINITION öööh!
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 2..3
/label=öööh!
/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_)
assert str(a.seq)=="ACGT"
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_synced3(self):
pGUP1 = read("pGUP1_correct.gb")
pGREG505 = read("pGREG505.gb")
pGUP1_not_synced = read("pGUP1_not_synced.gb")
self.assertEqual(pGUP1_not_synced.synced(pGREG505).seguid(), '42wIByERn2kSe_Exn405RYwhffU')
def test_read_from_string():
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_)
assert str(a.seq) == "ACGT"
input_ = '''>hej
acgt'''
assert str(a.seq) == "ACGT"
input_ = u'''
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_)
assert str(a.seq) == "ACGT"
input_ = u'''>hej
acgt'''
assert str(a.seq) == "ACGT"
input_ = u'''>hej öööh!
acgt'''
assert str(a.seq) == "ACGT"
input_ = u'''
LOCUS New_DNA 4 bp ds-DNA linear 30-MAR-2013
DEFINITION öööh!
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 2..3
/label=öööh!
/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_)
assert str(a.seq) == "ACGT"
def test_parse1(self):
''' test parsing fasta sequences from a text'''
text = '''
points....: 1
The sequence seq below represents a double stranded linear DNA molecule.
>seq
CTCCCCTATCACCAGGGTACCGATAGCCACGAATCT
Give the sequence(s) of the fragment(s) formed after digesting seq
with the restriction enzyme Acc65I in the order that they appear in seq.
Use FASTA format and give the Watson strand(s) in 5'-3' direction below.
Give the sequences the names frag1,frag2,... etc.
>frag1
CTCCCCTATCACCAGG
>frag2
GTACCGATAGCCACGAATCT
*********** Question 4 ***********
QuestionID:
'''
result = parse(text)
correct = ['CTCCCCTATCACCAGGGTACCGATAGCCACGAATCT',
'CTCCCCTATCACCAGG',
'GTACCGATAGCCACGAATCT']
self.assertEqual( [str(s.seq) for s in result], correct )
self.assertEqual( [s.linear for s in result], [True,True,True] )
input = '''
LOCUS ScCYC1 330 bp DNA UNK 01-JAN-1980
DEFINITION ScCYC1
ACCESSION ScCYC1
VERSION ScCYC1
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 ATGACTGAAT TCAAGGCCGG TTCTGCTAAG AAAGGTGCTA CACTTTTCAA GACTAGATGT
61 CTACAATGCC ACACCGTGGA AAAGGGTGGC CCACATAAGG TTGGTCCAAA CTTGCATGGT
121 ATCTTTGGCA GACACTCTGG TCAAGCTGAA GGGTATTCGT ACACAGATGC CAATATCAAG
181 AAAAACGTGT TGTGGGACGA AAATAACATG TCAGAGTACT TGACTAACCC AAAGAAATAT
241 ATTCCTGGTA CCAAGATGGC CTTTGGTGGG TTGAAGAAGG AAAAAGACAG AAACGACTTA
301 ATTACCTACT TGAAAAAAGC CTGTGAGTAA
//
'''
result = parse(input).pop()
self.assertEqual( str(result.seq) , str(read(input).seq) )
correct = '''ATGACTGAATTCAAGGCCGGTTCTGCTAAGAAAGGTGCTACACTTTTCAAGACTAGATGTCTACAATGCCACACCGTGGAAAAGGGTGGCCCACATAAGGTTGGTCCAAACTTGCATGGTATCTTTGGCAGACACTCTGGTCAAGCTGAAGGGTATTCGTACACAGATGCCAATATCAAGAAAAACGTGTTGTGGGACGAAAATAACATGTCAGAGTACTTGACTAACCCAAAGAAATATATTCCTGGTACCAAGATGGCCTTTGGTGGGTTGAAGAAGGAAAAAGACAGAAACGACTTAATTACCTACTTGAAAAAAGCCTGTGAGTAA'''
self.assertEqual( str(result.seq) , correct )
self.assertTrue( result.linear == True )
self.assertTrue( result.circular == False )
seqs = parse('./RefDataBjorn.fas')
self.assertEqual( len(seqs) , 771 )
self.assertEqual( list(set([len (a) for a in seqs])) ,[901])
pAG25 = read("./pAG25.gb")
self.assertTrue( pAG25.circular == True )
self.assertTrue( pAG25.linear == False)
pCAPs = read("./pCAPs.gb")
self.assertTrue( pCAPs.circular == True )
self.assertTrue( pCAPs.linear == False)
pUC19 = read("./pUC19.gb")
self.assertTrue( pUC19.circular == True )
self.assertTrue( pUC19.linear == False)
from time import gmtime, strftime
import zipfile
import cStringIO
import sys
import os
import errno
import codecs
from docutils.core import publish_string
from docutils.writers.html4css1 import Writer as HisWriter
from pkg_resources import resource_filename
from Bio.Restriction import ZraI, AjiI, EcoRV
import pydna
pYPKa = pydna.read( resource_filename('ypkpathway', os.path.join('data', 'pYPKa.txt')))
pYPK0 = pydna.read( resource_filename('ypkpathway', os.path.join('data', 'pYPK0.txt')))
pYPKpw = pydna.read( resource_filename('ypkpathway', os.path.join('data', 'pYPKpw.txt')))
(p577,
p578,
p468,
p467,
p567,
p568,
p775,
p778,
p342) = pydna.parse( u''' >577
gttctgatcctcgagcatcttaagaattc
>578
def test_copy_features(self):
from pydna.utils import seguid
from pydna import read,copy_features
a=read("./pCAPs.gb")
b=read("./pCAPs_fasta.txt")
for sh in [1,2,3,3127,3128,3129]:
newb = (b[sh:]+b[:sh]).looped()
copy_features(a, newb)
#print "a",[len(str(f.extract(a).seq.lower()) for f in a.features if len(f)>10]
#print "b",[len(str(f.extract(newb).seq).lower()) for f in newb.features]
self.assertTrue( sorted([str(f.extract(a).seq).lower() for f in a.features if len(f)>10],key=len)
== sorted([str(f.extract(newb).seq).lower() for f in newb.features],key=len))
b=b.rc()
for sh in [1,2,3,3127,3128,3129]:
newb = b[sh:]+b[:sh]
copy_features(a, newb)
self.assertTrue( sorted([str(f.extract(a).seq).lower() for f in a.features if len(f)>10],key=len) == sorted([str(f.extract(newb).seq).lower() for f in newb.features],key=len))
seguid_bla = "riT98j2v4NxVS8sbw_Q8epCwQwo"
seguid_cre = "xLZ2xs2O8CUMmWh2OrhmNFp5ZLg"
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("attaacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("ttaacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("taacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("gttaccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("ttaccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("taccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,]
pYPKa = pydna.read('''
LOCUS pYPKa 3128 bp DNA circular UNK 08-MAY-2015
DEFINITION Product_568_pCAPsAjiIR (22-mer)_567_pCAPsAjiIF (23-mer)
cSEGUID_aV1eIrzOiCjvw01yvKkxDXHKLMk_2015-05-08T16:41:28.034624
ACCESSION 3128bp TmU_6uVdgKq5aQhTpHux7dVk9J8
VERSION 3128bp TmU_6uVdgKq5aQhTpHux7dVk9J8
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
primer_bind complement(558..578)
/note="567_pCAPsAjiIF"
/ApEinfo_fwdcolor="green"
/ApEinfo_revcolor="red"
misc complement(558..580)
/label="567_pCAPsAjiIF"
misc 581..602
/label="568_pCAPsAjiIR"
primer_bind 583..602
/note="568_pCAPsAjiIR"
/ApEinfo_fwdcolor="green"
/ApEinfo_revcolor="red"
rep_origin 1313
/direction=BOTH
gene complement(2072..2932)
/gene="bla"
CDS complement(2072..2932)
/product="beta-lactamase"
/codon_start=1
/transl_table=11
/db_xref="GI:2769263"
/db_xref="GOA:Q79DR3"
/db_xref="HSSP:P62593"
/db_xref="InterPro:IPR000871"
/db_xref="InterPro:IPR001466"
/db_xref="InterPro:IPR012338"
/db_xref="UniProtKB/TrEMBL:Q79DR3"
/translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
LIKHW"
/gene="bla"
/protein_id="CAA04868.1"
ORIGIN
1 tcgcgcgttt cggtgatgac ggtgaaaacc tctgacacat gcagctcccg gagacggtca
61 cagcttgtct gtaagcggat gccgggagca gacaagcccg tcagggcgcg tcagcgggtg
121 ttggcgggtg tcggggctgg cttaactatg cggcatcaga gcagattgta ctgagagtgc
181 accatagatc ctgaggatcg gggtgataaa tcagtctgcg ccacatcggg ggaaacaaaa
241 tggcgcgaga tctaaaaaaa aaggctccaa aaggagcctt tcgcgctacc aggtaacgcg
301 ccactccgac gggattaacg agtgccgtaa acgacgatgg ttttaccgtg tgcggagatc
361 aggttctgat cctcgagcat cttaagaatt cgtcccacgg tttgtctaga gcagccgaca
421 atctggccaa tttcctgacg ggtaattttg atttgcatgc cgtccgggtg agtcatagcg
481 tctggttgtt ttgccagatt cagcagagtc tgtgcaatgc ggccgctgac gtcgaggaac
541 gccaggttgc ccactttctc actagtgacc tgcagccgac gtgccatctg tgcagacaaa
601 cgcatcagga tatccggatt tacctgaatc aattggcgaa attttttgta cgaaatttca
661 gccacttcac aggcggtttt cgcacgtacc catgcgctac gttcctggcc ctcttcaaac
721 aggcccagtt cgccaataaa atcaccctga ttcagatagg agaggatcat ttctttaccc
781 tcttcgtctt tgatcagcac tgccacagag cctttaacga tgtagtacag cgtttccgct
841 ttttcaccct ggtgaataag cgtgctcttg gatgggtact tatgaatgtg gcaatgagac
901 aagaaccatt cgagagtagg atccgtttga ggtttaccaa gtaccataag atccttaaat
961 ttttattatc tagctagatg ataatattat atcaagaatt gtacctgaaa gcaaataaat
1021 tttttatctg gcttaactat gcggcatcag agcagattgt actgagagtg caccatatgc
1081 ggtgtgaaat accgcacaga tgcgtaagga gaaaataccg catcaggcgc tcttccgctt
1141 cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta tcagctcact
1201 caaaggcggt aatacggtta tccacagaat caggggataa cgcaggaaag aacatgtgag
1261 caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg tttttccata
1321 ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg tggcgaaacc
1381 cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg cgctctcctg
1441 ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga agcgtggcgc
1501 tttctcatag ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc tccaagctgg
1561 gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt aactatcgtc
1621 ttgagtccaa cccggtaaga cacgacttat cgccactggc agcagccact ggtaacagga
1681 ttagcagagc gaggtatgta ggcggtgcta cagagttctt gaagtggtgg cctaactacg
1741 gctacactag aaggacagta tttggtatct gcgctctgct gaagccagtt accttcggaa
1801 aaagagttgg tagctcttga tccggcaaac aaaccaccgc tggtagcggt ggtttttttg
1861 tttgcaagca gcagattacg cgcagaaaaa aaggatctca agaagatcct ttgatctttt
1921 ctacggggtc tgacgctcag tggaacgaaa actcacgtta agggattttg gtcatgagat
1981 tatcaaaaag gatcttcacc tagatccttt taaattaaaa atgaagtttt aaatcaatct
2041 aaagtatata tgagtaaact tggtctgaca gttaccaatg cttaatcagt gaggcaccta
2101 tctcagcgat ctgtctattt cgttcatcca tagttgcctg actccccgtc gtgtagataa
2161 ctacgatacg ggagggctta ccatctggcc ccagtgctgc aatgataccg cgagacccac
2221 gctcaccggc tccagattta tcagcaataa accagccagc cggaagggcc gagcgcagaa
2281 gtggtcctgc aactttatcc gcctccatcc agtctattaa ttgttgccgg gaagctagag
2341 taagtagttc gccagttaat agtttgcgca acgttgttgc cattgctaca ggcatcgtgg
2401 tgtcacgctc gtcgtttggt atggcttcat tcagctccgg ttcccaacga tcaaggcgag
2461 ttacatgatc ccccatgttg tgcaaaaaag cggttagctc cttcggtcct ccgatcgttg
2521 tcagaagtaa gttggccgca gtgttatcac tcatggttat ggcagcactg cataattctc
2581 ttactgtcat gccatccgta agatgctttt ctgtgactgg tgagtactca accaagtcat
2641 tctgagaata gtgtatgcgg cgaccgagtt gctcttgccc ggcgtcaata cgggataata
2701 ccgcgccaca tagcagaact ttaaaagtgc tcatcattgg aaaacgttct tcggggcgaa
2761 aactctcaag gatcttaccg ctgttgagat ccagttcgat gtaacccact cgtgcaccca
2821 actgatcttc agcatctttt actttcacca gcgtttctgg gtgagcaaaa acaggaaggc
2881 aaaatgccgc aaaaaaggga ataagggcga cacggaaatg ttgaatactc atactcttcc
2941 tttttcaata ttattgaagc atttatcagg gttattgtct catgagcgga tacatatttg
3001 aatgtattta gaaaaataaa caaatagggg ttccgcgcac atttccccga aaagtgccac
3061 ctgctaagaa accattatta tcatgacatt aacctataaa aataggcgta tcacgaggcc
3121 ctttcgtc
//
''')
67 4249–4255.
'''
raw_input("press return!\n")
gb=Genbank("*****@*****.**")
if gb.test():
xks1_gene = gb.nucleotide("Z72979")
print "Genbank record Z72979 downloaded from NCBI"
YEp24PGK = gb.nucleotide("KC562906")
print "Genbank record KC562906 downloaded from NCBI\n"
else:
xks1_gene = read("Z72979.gb")
print "A local copy of Genbank record Z72979 is used"
YEp24PGK = read("KC562906.gb")
print "A local copy of Genbank record KC562906 is used\n"
raw_input("press return!\n")
primers='''
>primer1
GCGGATCCTCTAGAATGGTTTGTTCAGTAATTCAG
>primer3
AGATCTGGATCCTTAGATGAGAGTCTTTTCCAG
'''
primer1, primer2 = parse(primers, ds=False)
xks1_pcr_product = pcr(primer1, primer2, xks1_gene)
Open fasta format file and returns the sequence.
"""
f = SeqIO.parse(open(fasta, 'rU'), 'fasta').next()
return f.seq
#######################################################
gb = pydna.Genbank("*****@*****.**") # Tell Genbank who you are!
gene = gb.nucleotide("X06997") # Kluyveromyces lactis LAC12 gene for lactose permease.
#######################################################
genome = pydna.read('FSC237.fasta')
#genome = fasta_seq('FSC237.fasta')
primer_f,primer_r = pydna.parse(''' >B4_400_1-F
AGCAGTGCCTGTTGTACC
>B4_400_1-R
AGTTTCTCAACATGGAAT
''', ds=False)
pcr_prod = pydna.pcr(primer_f,primer_r, genome)
#stssearch -seqall genome.fasta -infile primers.txt -stdout --auto
primersearch -seqall genome.fasta -infile primers.txt -mismatchpercent 1 -stdout --auto -mismatchpercent 10
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_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_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_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_parse1(self):
''' test parsing fasta sequences from a text'''
text = '''
points....: 1
The sequence seq below represents a double stranded linear DNA molecule.
>seq
CTCCCCTATCACCAGGGTACCGATAGCCACGAATCT
Give the sequence(s) of the fragment(s) formed after digesting seq
with the restriction enzyme Acc65I in the order that they appear in seq.
Use FASTA format and give the Watson strand(s) in 5'-3' direction below.
Give the sequences the names frag1,frag2,... etc.
>frag1
CTCCCCTATCACCAGG
>frag2
GTACCGATAGCCACGAATCT
*********** Question 4 ***********
QuestionID:
'''
result = parse(text)
correct = [
'CTCCCCTATCACCAGGGTACCGATAGCCACGAATCT', 'CTCCCCTATCACCAGG',
'GTACCGATAGCCACGAATCT'
]
self.assertEqual([str(s.seq) for s in result], correct)
self.assertEqual([s.linear for s in result], [True, True, True])
input = '''
LOCUS ScCYC1 330 bp DNA UNK 01-JAN-1980
DEFINITION ScCYC1
ACCESSION ScCYC1
VERSION ScCYC1
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 ATGACTGAAT TCAAGGCCGG TTCTGCTAAG AAAGGTGCTA CACTTTTCAA GACTAGATGT
61 CTACAATGCC ACACCGTGGA AAAGGGTGGC CCACATAAGG TTGGTCCAAA CTTGCATGGT
121 ATCTTTGGCA GACACTCTGG TCAAGCTGAA GGGTATTCGT ACACAGATGC CAATATCAAG
181 AAAAACGTGT TGTGGGACGA AAATAACATG TCAGAGTACT TGACTAACCC AAAGAAATAT
241 ATTCCTGGTA CCAAGATGGC CTTTGGTGGG TTGAAGAAGG AAAAAGACAG AAACGACTTA
301 ATTACCTACT TGAAAAAAGC CTGTGAGTAA
//
'''
result = parse(input).pop()
self.assertEqual(str(result.seq), str(read(input).seq))
correct = '''ATGACTGAATTCAAGGCCGGTTCTGCTAAGAAAGGTGCTACACTTTTCAAGACTAGATGTCTACAATGCCACACCGTGGAAAAGGGTGGCCCACATAAGGTTGGTCCAAACTTGCATGGTATCTTTGGCAGACACTCTGGTCAAGCTGAAGGGTATTCGTACACAGATGCCAATATCAAGAAAAACGTGTTGTGGGACGAAAATAACATGTCAGAGTACTTGACTAACCCAAAGAAATATATTCCTGGTACCAAGATGGCCTTTGGTGGGTTGAAGAAGGAAAAAGACAGAAACGACTTAATTACCTACTTGAAAAAAGCCTGTGAGTAA'''
self.assertEqual(str(result.seq), correct)
self.assertTrue(result.linear == True)
self.assertTrue(result.circular == False)
seqs = parse('./RefDataBjorn.fas')
self.assertEqual(len(seqs), 771)
self.assertEqual(list(set([len(a) for a in seqs])), [901])
pAG25 = read("./pAG25.gb")
self.assertTrue(pAG25.circular == True)
self.assertTrue(pAG25.linear == False)
pCAPs = read("./pCAPs.gb")
self.assertTrue(pCAPs.circular == True)
self.assertTrue(pCAPs.linear == False)
pUC19 = read("./pUC19.gb")
self.assertTrue(pUC19.circular == True)
self.assertTrue(pUC19.linear == False)
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))
cloning in yeast. Gene, 344: 43–51.
http://www.ncbi.nlm.nih.gov/pubmed/15656971
'''
print info
raw_input("Press any key and wait for the script to finish!")
# Establish the two primers. These sequences can be found in (1)
GUP1rec1sens = SeqRecord(Seq("gaattcgatatcaagcttatcgataccgatgtcgctgatcagcatcctgtctcc"))
GUP1rec2AS = SeqRecord(Seq("gacataactaattacatgactcgaggtcgactcagcattttaggtaaattccg"))
# Read the GUP1 locus sequence into a Dseqrecord object
# This sequence was taken from the Saccharomyces genome Database:
# http://www.yeastgenome.org/cgi-bin/getSeq?query=YGL084C&flankl=1000&flankr=1000&format=fasta
GUP1 = read("GUP1_locus.gb")
# The insert is formed by PCR using the two primers and the template sequence
insert = pcr(GUP1rec1sens, GUP1rec2AS, GUP1)
# The sequence for the plasmid is read into a Dseqrecord object called pGREG505
# this sequence was found at
# http://www.euroscarf.de/plasmid_details.php?accno=P30350
# This sequence is circular, this information is parsed from the Genbank file.
pGREG505 = read("pGREG505.gb")
# Import the SalI restriction enzyme from Biopython
from Bio.Restriction import SalI
# Cut the circular pGREG505 plasmid with SalI
# this enzyme cuts twice, so two fragments are formed
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())
''' Thanks to Min RK, UC Berkeley for this'''
def _repr_pretty_(self, p, cycle):
p.text(self)
class pretty_unicode(unicode):
def _repr_pretty_(self, p, cycle):
p.text(self)
class pretty_string(str):
def _repr_pretty_(self, p, cycle):
p.text(self)
if __name__=="__main__":
import pydna
print pydna.read("/home/bjorn/Desktop/python_packages/pydna/pydna/pydna_read_test.txt").format()
print pydna.read("/home/bjorn/Desktop/python_packages/pydna/pydna/pydna_read_test2.txt").format()[3270:3281]
import sys;sys.exit(42)
import StringIO
from Bio import SeqIO
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
import textwrap, re
raw = open("pydna_read_test.txt", 'rU').read()
pattern = r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)"
rawseq = re.findall(pattern, textwrap.dedent(raw + "\n\n"), flags=re.MULTILINE).pop(0)
handle = StringIO.StringIO(raw)
Lignocellulosic Hydrolysate, Applied and Environmental Microbiology
67 4249–4255.
'''
raw_input("press return!\n")
gb = Genbank("*****@*****.**")
if gb.test():
xks1_gene = gb.nucleotide("Z72979")
print "Genbank record Z72979 downloaded from NCBI"
YEp24PGK = gb.nucleotide("KC562906")
print "Genbank record KC562906 downloaded from NCBI\n"
else:
xks1_gene = read("Z72979.gb")
print "A local copy of Genbank record Z72979 is used"
YEp24PGK = read("KC562906.gb")
print "A local copy of Genbank record KC562906 is used\n"
raw_input("press return!\n")
primers = '''
>primer1
GCGGATCCTCTAGAATGGTTTGTTCAGTAATTCAG
>primer3
AGATCTGGATCCTTAGATGAGAGTCTTTTCCAG
'''
primer1, primer2 = parse(primers, ds=False)
xks1_pcr_product = pcr(primer1, primer2, xks1_gene)
def test_copy_features(self):
from pydna.utils import seguid
from pydna import read, copy_features
a = read("./pCAPs.gb")
b = read("./pCAPs_fasta.txt")
for sh in [1, 2, 3, 3127, 3128, 3129]:
newb = (b[sh:] + b[:sh]).looped()
copy_features(a, newb)
#print "a",[len(str(f.extract(a).seq.lower()) for f in a.features if len(f)>10]
#print "b",[len(str(f.extract(newb).seq).lower()) for f in newb.features]
self.assertTrue(
sorted([
str(f.extract(a).seq).lower()
for f in a.features if len(f) > 10
],
key=len) ==
sorted(
[str(f.extract(newb).seq).lower() for f in newb.features],
key=len))
b = b.rc()
for sh in [1, 2, 3, 3127, 3128, 3129]:
newb = b[sh:] + b[:sh]
copy_features(a, newb)
self.assertTrue(
sorted([
str(f.extract(a).seq).lower()
for f in a.features if len(f) > 10
],
key=len) ==
sorted(
[str(f.extract(newb).seq).lower() for f in newb.features],
key=len))
seguid_bla = "riT98j2v4NxVS8sbw_Q8epCwQwo"
seguid_cre = "xLZ2xs2O8CUMmWh2OrhmNFp5ZLg"
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("attaacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("ttaacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("taacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq)
for f in b.features] == [seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("gttaccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("ttaccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("taccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [
seguid_cre,
seguid_cre,
]
class pretty_unicode(unicode):
def _repr_pretty_(self, p, cycle):
p.text(self)
class pretty_string(str):
def _repr_pretty_(self, p, cycle):
p.text(self)
if __name__ == "__main__":
import pydna
print pydna.read(
"/home/bjorn/Desktop/python_packages/pydna/pydna/pydna_read_test.txt"
).format()
print pydna.read(
"/home/bjorn/Desktop/python_packages/pydna/pydna/pydna_read_test2.txt"
).format()[3270:3281]
import sys
sys.exit(42)
import StringIO
from Bio import SeqIO
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
import textwrap, re
raw = open("pydna_read_test.txt", 'rU').read()
pattern = r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)"
"""
print info
raw_input("Press any key and wait for the script to finish!")
# Establish the two primers. These sequences can be found in (1)
GUP1rec1sens = SeqRecord(
Seq("gaattcgatatcaagcttatcgataccgatgtcgctgatcagcatcctgtctcc"))
GUP1rec2AS = SeqRecord(
Seq("gacataactaattacatgactcgaggtcgactcagcattttaggtaaattccg"))
# Read the GUP1 locus sequence into a Dseqrecord object
# This sequence was taken from the Saccharomyces genome Database:
# http://www.yeastgenome.org/cgi-bin/getSeq?query=YGL084C&flankl=1000&flankr=1000&format=fasta
GUP1 = read("GUP1_locus.gb")
# The insert is formed by PCR using the two primers and the template sequence
insert = pcr(GUP1rec1sens, GUP1rec2AS, GUP1)
# The sequence for the plasmid is read into a Dseqrecord object called pGREG505
# this sequence was found at
# http://www.euroscarf.de/plasmid_details.php?accno=P30350
# This sequence is circular, this information is parsed from the Genbank file.
pGREG505 = read("pGREG505.gb")
# Import the SalI restriction enzyme from Biopython
from Bio.Restriction import SalI
# Cut the circular pGREG505 plasmid with SalI
# this enzyme cuts twice, so two fragments are formed
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) )