def test_primer_Design():
''' test_primer_design'''
a=Dseqrecord("atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg")
b=Dseqrecord("ccaaacccaccaggtaccttatgtaagtacttcaagtcgccagaagacttcttggtcaagttgcc")
c=Dseqrecord("tgtactggtgctgaaccttgtatcaagttgggtgttgacgccattgccccaggtggtcgtttcgtt")
primer_pairs = assembly_primers([a,b,c])
frags=[]
for (f,r),t in zip(primer_pairs,[a,b,c]):
frags.append(pcr(f,r,t))
asm=Assembly(frags)
assert asm.linear_products[0].seguid() == "1eNv3d_1PqDPP8qJZIVoA45Www8"
frags=[]
primer_pairs = assembly_primers([a,b,c], circular=True)
for (f,r),t in zip(primer_pairs,[a,b,c]):
frags.append(pcr(f,r,t))
#print frags
asm=Assembly(frags)
assert asm.circular_products[0].cseguid() == "V3Mi8zilejgyoH833UbjJOtDMbc"
def test_primer_Design_with_linker(self):
''' test_primer_design'''
from pydna import Dseqrecord, Assembly, pcr, assembly_primers
b = Dseqrecord("agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord("tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
((bf,br),(cf,cr)) = assembly_primers((b,l,c))
nb = pcr((bf,br),b)
nc = pcr((cf,cr),c)
asm1 = Assembly((nb,nc))
self.assertEqual(asm1.linear_products[0].seguid(),(b+l+c).seguid(),'l95igKB8iKAKrvvqE9CYksyNx40')
b = Dseqrecord("agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord("tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
((bf,br),(cf,cr)) = assembly_primers((b,l,c), circular = True)
nb = pcr((bf,br),b)
nc = pcr((cf,cr),c)
asm = Assembly((nb,nc))
self.assertEqual((b+l+c).looped().cseguid(), asm.circular_products[0].cseguid(), 'qMEHxKkTsWIXkbqGA5O35631eMU')
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_primer_Design_with_linker():
''' test_primer_design'''
from pydna import Dseqrecord, Assembly, pcr, assembly_primers
b = Dseqrecord("agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord("tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
((bf,br),(cf,cr)) = assembly_primers((b,l,c))
nb = pcr((bf,br),b)
nc = pcr((cf,cr),c)
asm1 = Assembly((nb,nc))
assert asm1.linear_products[0].seguid(),(b+l+c).seguid() == 'l95igKB8iKAKrvvqE9CYksyNx40'
b = Dseqrecord("agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord("tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
((bf,br),(cf,cr)) = assembly_primers((b,l,c), circular = True)
nb = pcr((bf,br),b)
nc = pcr((cf,cr),c)
asm = Assembly((nb,nc))
#print (b+l+c).looped().seq
assert (b+l+c).looped().cseguid() == asm.circular_products[0].cseguid()
#print (b+l+c).looped().cseguid() == 'jdHXfQI5k4Sk2ESiZYfKv4oP2FI'
assert (b+l+c).looped().cseguid() == 'jdHXfQI5k4Sk2ESiZYfKv4oP2FI'
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 test_circ_pcr(self):
''' test circ pcr'''
s = parse('''
>MCT4_flaghis_rv
gccgcaagcttgtcgtcatcgtctttgtagtcCATggccaggagggttggttccgcc
>MCT4_flaghis_fw
ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggcc''', ds=False)
t = parse('''
>hej circular
TCAGGTGAGGCGGAACCAACCCTCCTGGCCATGggaggggccgtggtggacgagggccccacaggcg
''')
p = pcr(s,t)
self.assertTrue( p.seguid() == 'wYEpbWxO8tfgA_AL67wqGzYmc5k')
def test_circ_pcr(self):
''' test circ pcr'''
s = parse('''
>MCT4_flaghis_rv
gccgcaagcttgtcgtcatcgtctttgtagtcCATggccaggagggttggttccgcc
>MCT4_flaghis_fw
ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggcc''',
ds=False)
t = parse('''
>hej circular
TCAGGTGAGGCGGAACCAACCCTCCTGGCCATGggaggggccgtggtggacgagggccccacaggcg
''')
p = pcr(s, t)
self.assertTrue(p.seguid() == 'wYEpbWxO8tfgA_AL67wqGzYmc5k')
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_pcr(self):
''' test pcr'''
raw = []
raw.append((
'7JOV1MJBZJp2Smja/7KFGhS2SWY',
parse('''
>524_pFA6aF (29-mer)
cacatacgatttaggtgacactatagaac
>523_AgTEF1tpR (21-mer)
ggttgtttatgttcggatgtg
'''),
parse("./pAG25.gb"),
))
raw.append((
'7pPxy/bQvs4+7CaOgiywQVzUFDc',
parse('''
>lowgc_f
TTTCACTAGTTACTTGTAGTCGacgtgccatctgtgcagacaaacgcatcaggatat
>lowgc_r
AAGTTGGAAATCTAGCTTTTCTTgacgtcagcggccgcattgcaca
'''),
parse("./pCAPs.gb"),
))
raw.append((
'7JOV1MJBZJp2Smja/7KFGhS2SWY',
parse('''
>524_pFA6aF (29-mer)
cacatacgatttaggtgacactatagaac
>523_AgTEF1tpR (21-mer)
ggttgtttatgttcggatgtg
'''),
parse("../tests/pAG25.gb"),
))
raw.append((
'yshvYTXr9iXCnh3YytWQRDBNQzI',
parse('''
>ForwardPrimer1
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg
LOCUS sequence_50_bp 46 bp DNA circular UNK 08-FEB-2013
DEFINITION sequence_50_bp circular
ACCESSION sequence_50_bp
VERSION sequence_50_bp
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 ccaagataga gtcagtaacc acagctacta cacacgtact gactgt
//
'''),
))
raw.append((
'yshvYTXr9iXCnh3YytWQRDBNQzI',
parse('''
>ForwardPrimer2
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg
LOCUS template 46 bp DNA circular UNK 15-OCT-2012
DEFINITION template circular
ACCESSION template
VERSION template
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 ccaagataga gtcagtaacc acagctacta cacacgtact gactgt
//
'''),
))
raw.append((
'yshvYTXr9iXCnh3YytWQRDBNQzI',
parse('''
>ForwardPrimer3
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg
LOCUS template 46 bp DNA circular UNK 08-FEB-2013
DEFINITION template circular
ACCESSION template
VERSION template
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 tccaagatag agtcagtaac cacagctact acacacgtac tgactg
//
'''),
))
raw.append((
'yshvYTXr9iXCnh3YytWQRDBNQzI',
parse('''
>ForwardPrimer4
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg
LOCUS template 46 bp DNA circular UNK 15-OCT-2012
DEFINITION template circular
ACCESSION template
VERSION template
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 gtccaagata gagtcagtaa ccacagctac tacacacgta ctgact
//
'''),
))
raw.append((
'60meNXeGKO7ahZwcIl5yXHFC3Yg',
parse('''
>fw1
cacatacgatttaggtgacactatagaac
>rv
ggttgtttatgttcggatgtg
LOCUS tm 50 bp DNA circular UNK 15-OCT-2012
DEFINITION tm circular
ACCESSION tm
VERSION tm
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 cacatccgaa cataaacaac ccacatacga tttaggtgac actatagaac
//
'''),
))
raw.append((
'60meNXeGKO7ahZwcIl5yXHFC3Yg',
parse('''
>fw2
cacatacgatttaggtgacactatagaac
>rv
ggttgtttatgttcggatgtg
LOCUS tm 50 bp DNA circular UNK 15-OCT-2012
DEFINITION tm circular
ACCESSION tm
VERSION tm
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 acatccgaac ataaacaacc cacatacgat ttaggtgaca ctatagaacc
//
'''),
))
raw.append((
'60meNXeGKO7ahZwcIl5yXHFC3Yg',
parse('''
>fw3
cacatacgatttaggtgacactatagaac
>rv
ggttgtttatgttcggatgtg
LOCUS tm 50 bp DNA circular UNK 15-OCT-2012
DEFINITION tm circular
ACCESSION tm
VERSION tm
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 ccacatccga acataaacaa cccacatacg atttaggtga cactatagaa
//
'''),
))
raw.append((
'y6ohCJ4O+8Is012DItz4F4saxNo',
parse('''
>f_Eric_Ma
ARATGAGTCTTCTRACCGAGGTCG
>r_Eric_Ma
TGAAAAGACATCYTCAAGYYTCTG
>templ
AGCAAAAGCAGGTAGATATTGAAAAATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCGTCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTCTCTGCAGGGAAGAACACTGATCTCGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAGAATGCCTTAAATGGGAATGGAGACCCAAACAACATGGACAGGGCAGTCAAACTATACAGGAAGCTGAAAAGAGAGATAACATTCCATGGGGCTAAAGAGGTTGCACTCAGCTATTCAACCGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTAACCACAGAAGTAGCTTTTGGCCTGGTGTGTGCCACTTGTGAGCAGATTGCTGACTCACAGCATCGATCTCACAGACAGATGGTGACTACCACCAACCCACTAATCAGGCATGAAAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCTGGATCGAGTGAACAGGCAGCGGAAGCCATGGAGGTTGCTAGTCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCACCCTAGCTCCAGTGCCGGTCTGAAAGATGATCTTCTTGAAAATTTGCAGGCCTACCAGAAGCGGATGGGAGTGCAAATGCAGCGATTCAAGTGATCCTCTCGTTATTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCCTTTCTTCAAATGTATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAGTGCCTGAGTCTATGAGGGAAGAGTATCGGCAGGAACAGCAGAGTGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCTTGTTTCTACT
'''),
))
for key, tst in enumerate(raw):
print key
print tst[1][0].name
print "pcr test", key
print
self.assertEqual(tst[0], seguid(pcr(tst[1:]).seq))
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
linear_vector, his3 = pGREG505.cut(SalI)
# Circular recombination products are formed
for insertname, pf, pr, status in (x.split() for x in tps.split("\n")):
print "in:", letter, insertname, pf, pr,
fp = lp.primer[int(pf)]
rp = lp.primer[int(pr)]
gbref = sg.gene[insertname.upper()].promoter().description
gblink = sg.gene[insertname.upper()].cds().id
template = pydna.Dseqrecord(sg.gene[insertname.upper()].promoter())
templatesize = len(template)
insertseguid = template.seguid()
finalcseguid = (pYPKa.linearize(enz)+pydna.pcr(fp, rp, template)).looped().cseguid()
#import sys;sys.exit()
r = t.format( tp = insertname,
enz=repr(enz),
gbref = gbref,
gblink =gblink,
templatesize = templatesize,
insertseguid = insertseguid,
finalcseguid = finalcseguid,
fpn=fp.name,
fps=fp.seq,
rpn=rp.name,
rps=rp.seq)
def __init__(self, enzyme, data):
fp_tail = "ttaaat"
rp_tail = "taattaa"
if enzyme == ZraI:
fp = p577
rp = p342
desc_re = re.compile("pYPKa_Z_([^\d\W]\w{2,15})tp")
self.letter = "Z"
elif enzyme == AjiI:
fp = p468
rp = p342
fp_tail = "aa"
rp_tail = ""
desc_re = re.compile("pYPKa_A_([^\d\W]\w{2,15})")
self.letter = "A"
elif enzyme == EcoRV:
fp = p568
rp = p342
desc_re = re.compile("pYPKa_E_([^\d\W]\w{2,15})tp")
self.letter = "E"
else:
raise Exception(u"Enzyme has to be ZraI, Ajii or EcoRV, but got {}".format(enzyme))
self.enzyme = enzyme
self.insert_length = cloned(pYPKa, enzyme, data)
if self.insert_length:
m = desc_re.search(data.description)
if not m:
raise Exception(u"{} is a pYPKa_{} sequence but was not correctly named.".format(data.description,
self.letter))
self.insert_description = m.group(1)
self.name = m.group(0)
self.code = "{} = read('{}.txt')".format({ "Z":"first",
"A":"middle",
"E":"last"}[self.letter],
self.name)
self.files = { "{}.txt".format(self.name) : data.format("gb").encode("utf-8"),
"{}_plan.rst".format(self.name) : u"This vector was given!"}
self.rec = data
self.flag = True
elif data.linear:
self.insert_description = data.name # .id .description
f,r = pydna.cloning_primers(data,
minlength=pYPKa_clone.minlength,
maxlength=pYPKa_clone.maxlength,
fp_tail=fp_tail,
rp_tail=rp_tail)
self.insert = pydna.pcr(f, r, data)
self.insert_length = len(self.insert)
self.insert.description+= "_prd"
self.name = u"pYPKa_{}_{}{}".format(self.letter,
data.name.split("tp")[0],
{ZraI : "tp",
AjiI : "",
EcoRV: "tp" }[enzyme])
code = pYPKa_clone.codetempl.format( enz = self.enzyme,
tp = data.name,
f = f.format("fasta"),
r = r.format("fasta"),
vn = self.name)
self.rec = (pYPKa.linearize(self.enzyme) + self.insert).looped().synced("tcgcgcgtttcggtgatgacggtgaaaacctctg")
self.rec_rv = (pYPKa.linearize(self.enzyme) + self.insert.rc()).looped().synced("tcgcgcgtttcggtgatgacggtgaaaacctctg")
self.rec.id = self.name[:15]
self.rec.description = self.name
plan = pYPKa_clone.plantempl.format( template = u"{}_template".format(data.name),
rec = self.name,
fwd = self.insert.forward_primer.name,
rev = self.insert.reverse_primer.name,
figure = add_space(self.insert.figure()),
program = add_space(self.insert.program()),
pcr_product =self.insert_description,
length = len(self.insert),
enz=enzyme,
name = self.name,
line = "="*len(self.name),
fp = fp.name,
rp = rp.name,
f = f.name,
correct_products = ", ".join(str(f) for f in [len(p) for p in pydna.Anneal((fp,rp,f), self.rec).products]),
reversed_products = ", ".join(str(f) for f in [len(p) for p in pydna.Anneal((fp,rp,f), self.rec_rv).products]),
clone_empty = ", ".join(str(f) for f in [len(p) for p in pydna.Anneal((fp,rp,f), pYPKa).products]))
self.files = { "{}_template.txt".format(data.name) : data.format("gb").decode("utf-8"),
"{}.txt".format(self.insert_description) : self.insert.format("gb").decode("utf-8"),
"{}.txt".format(self.name) : self.rec.format("gb").decode("utf-8"),
"{}.py".format(self.name) : code,
"{}_plan.rst".format(self.name) : plan}
self.code = "from {0} import {0} as {1}".format(self.name,
{ZraI : "first",
AjiI : "middle",
EcoRV: "last" }[enzyme])
self.flag = False
else:
raise Exception("{} has to be a linear DNA fragment or a pYPKa_{} clone!".format(data.description,
self.letter))
def right_product(self):
return pydna.pcr(p775, p578, self.seq)
def assembly_product(self):
return pydna.pcr(p775, p778, self.seq)
def left_product(self):
return pydna.pcr(p577, p778, self.seq)
def __init__(self, *args):
self.pYPKa_ZraI_tp1 = None
self.pYPKa_AjiI_gene = None
self.pYPKa_EcoRV_tp2 = None
if len(args)==1:
self.seq = args[0]
m = pYPK0_tp_gene_tp.desc_re.search(self.seq.description)
if not m:
raise Exception( "{} is a pYPK0 tp-gene_tp sequence but was not correctly named.".format(last.description))
self.tp1_description = m.group(1)
self.gene_description = m.group(2)
self.tp2_description = m.group(3)
self.pYPKa_clones = []
self.seq.description = self.seq.description.replace(" ","_")
self.files = { "{}.txt".format(self.seq.description) : self.seq.format("gb"),
"{}_plan.rst".format(self.seq.description) : u"This vector was given!"}
self.code = "{i} = read('{f}')".format(f= "{}.txt".format(self.seq.description), i= "{}")
elif len(args)==3:
self.pYPKa_clones = [pYPKa_clone(ZraI, args[0]),
pYPKa_clone(AjiI, args[1]),
pYPKa_clone(EcoRV,args[2])]
first = pydna.pcr( p577, p567, self.pYPKa_clones[0].rec)
middle = pydna.pcr( p468, p467, self.pYPKa_clones[1].rec)
last = pydna.pcr( p568, p578, self.pYPKa_clones[2].rec)
self.assembly = pydna.Assembly([pYPK0_tp_gene_tp.pYPKpw_lin, first, middle, last], limit=31)
self.seq = self.assembly.circular_products[0]
self.tp1_description = self.pYPKa_clones[0].insert_description
self.gene_description = self.pYPKa_clones[1].insert_description
self.tp2_description = self.pYPKa_clones[2].insert_description
self.seq.name = "pYPK0_tp_gene_tp"
self.seq.id = "-"
#self.seq.annotations['source'] = "123" # SOURCE
#self.seq.annotations['organism'] = "123" # ORGANISM
#self.seq.annotations['comment'] = "123" # COMMENT
self.seq.description = "pYPK0_{}tp_{}_{}tp".format(self.pYPKa_clones[0].insert_description.split("tp")[0],
self.pYPKa_clones[1].insert_description,
self.pYPKa_clones[2].insert_description.split("tp")[0])
tp_gene_size = [len(p) for p in pydna.Anneal((p577,p467), self.seq).products]
gene_tp_size = [len(p) for p in pydna.Anneal((p468,p578), self.seq).products]
plan = pYPK0_tp_gene_tp.plantempl.format( name = self.seq.description,
tp1 = first.name,
gene = middle.name,
tp2 = last.name,
figure = add_space(self.seq.small_fig()),
pcr1=add_space(first.figure()),
pcr2=add_space(middle.figure()),
pcr3=add_space(last.figure()),
prg1=add_space(first.program()),
prg2=add_space(middle.program()),
prg3=add_space(last.program()),
tp1_name = self.pYPKa_clones[0].name+"_pcr_prd",
gene_name = self.pYPKa_clones[1].name+"_pcr_prd",
tp2_name = self.pYPKa_clones[2].name+"_pcr_prd",
tmp1 = self.pYPKa_clones[0].name,
tmp2 = self.pYPKa_clones[1].name,
tmp3 = self.pYPKa_clones[2].name,
line = "="*len(self.seq.description),
p1 = first.forward_primer.name,
p2 = first.reverse_primer.name,
p3 = middle.forward_primer.name,
p4 = middle.reverse_primer.name,
p5 = last.forward_primer.name,
p6 = last.reverse_primer.name,
correct_first_tp_gene_prd = ", ".join(str(s) for s in tp_gene_size),
missing_first_tp_prd = ", ".join(str(s-self.pYPKa_clones[0].insert_length) for s in tp_gene_size),
missing_gene_prd1 = ", ".join(str(s-self.pYPKa_clones[1].insert_length) for s in tp_gene_size),
empty_prd1 = ", ".join(str(s-self.pYPKa_clones[0].insert_length-self.pYPKa_clones[1].insert_length ) for s in tp_gene_size),
correct_gene_tp_prd = ", ".join(str(s) for s in gene_tp_size),
missing_gene_prd2 = ", ".join(str(s-self.pYPKa_clones[1].insert_length) for s in gene_tp_size),
missing_last_tp_prd = ", ".join(str(s-self.pYPKa_clones[2].insert_length) for s in gene_tp_size),
empty_prd2 = ", ".join(str(s-self.pYPKa_clones[1].insert_length-self.pYPKa_clones[2].insert_length) for s in gene_tp_size),)
code = [ self.pYPKa_clones[0].code,
self.pYPKa_clones[1].code,
self.pYPKa_clones[2].code]
code = pYPK0_tp_gene_tp.codetempl.format(code = "\n".join(code),
vn = self.seq.description)
self.files = {self.pYPKa_clones[0].name+"_pcr_prd.txt" : first.format("gb").decode("utf-8"),
self.pYPKa_clones[1].name+"_pcr_prd.txt" : middle.format("gb").decode("utf-8"),
self.pYPKa_clones[2].name+"_pcr_prd.txt" : last.format("gb").decode("utf-8"),
"{}.py".format(self.seq.description) : code,
"{}.txt".format(self.seq.description) : self.seq.synced("tcgcgcgtttcggtgatgacggtgaaaacctctg").format("gb").decode("utf-8"),
"{}_plan.rst".format(self.seq.description) : plan}
self.code = "from {i} import {i} as {c}".format(i=self.seq.description, c="{}")
else:
raise Exception("Either one or three arguments!")
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
linear_vector, his3 = pGREG505.cut(SalI)
# Circular recombination products are formed
def test_pcr(self):
''' test pcr'''
raw=[]
raw.append(
('7JOV1MJBZJp2Smja/7KFGhS2SWY',
parse('''
>524_pFA6aF (29-mer)
cacatacgatttaggtgacactatagaac
>523_AgTEF1tpR (21-mer)
ggttgtttatgttcggatgtg
'''),
parse("./pAG25.gb"),)
)
raw.append(
('7pPxy/bQvs4+7CaOgiywQVzUFDc',
parse('''
>lowgc_f
TTTCACTAGTTACTTGTAGTCGacgtgccatctgtgcagacaaacgcatcaggatat
>lowgc_r
AAGTTGGAAATCTAGCTTTTCTTgacgtcagcggccgcattgcaca
'''),
parse("./pCAPs.gb"),)
)
raw.append(
('7JOV1MJBZJp2Smja/7KFGhS2SWY',
parse('''
>524_pFA6aF (29-mer)
cacatacgatttaggtgacactatagaac
>523_AgTEF1tpR (21-mer)
ggttgtttatgttcggatgtg
'''),
parse("../tests/pAG25.gb"),
))
raw.append(
('yshvYTXr9iXCnh3YytWQRDBNQzI',
parse('''
>ForwardPrimer1
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg
LOCUS sequence_50_bp 46 bp DNA circular UNK 08-FEB-2013
DEFINITION sequence_50_bp circular
ACCESSION sequence_50_bp
VERSION sequence_50_bp
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 ccaagataga gtcagtaacc acagctacta cacacgtact gactgt
//
'''),))
raw.append(
('yshvYTXr9iXCnh3YytWQRDBNQzI',
parse('''
>ForwardPrimer2
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg
LOCUS template 46 bp DNA circular UNK 15-OCT-2012
DEFINITION template circular
ACCESSION template
VERSION template
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 ccaagataga gtcagtaacc acagctacta cacacgtact gactgt
//
'''),))
raw.append(
('yshvYTXr9iXCnh3YytWQRDBNQzI',
parse('''
>ForwardPrimer3
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg
LOCUS template 46 bp DNA circular UNK 08-FEB-2013
DEFINITION template circular
ACCESSION template
VERSION template
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 tccaagatag agtcagtaac cacagctact acacacgtac tgactg
//
'''),))
raw.append(
('yshvYTXr9iXCnh3YytWQRDBNQzI',
parse('''
>ForwardPrimer4
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg
LOCUS template 46 bp DNA circular UNK 15-OCT-2012
DEFINITION template circular
ACCESSION template
VERSION template
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 gtccaagata gagtcagtaa ccacagctac tacacacgta ctgact
//
'''),))
raw.append(
('60meNXeGKO7ahZwcIl5yXHFC3Yg',
parse('''
>fw1
cacatacgatttaggtgacactatagaac
>rv
ggttgtttatgttcggatgtg
LOCUS tm 50 bp DNA circular UNK 15-OCT-2012
DEFINITION tm circular
ACCESSION tm
VERSION tm
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 cacatccgaa cataaacaac ccacatacga tttaggtgac actatagaac
//
'''),)
)
raw.append(
('60meNXeGKO7ahZwcIl5yXHFC3Yg',
parse('''
>fw2
cacatacgatttaggtgacactatagaac
>rv
ggttgtttatgttcggatgtg
LOCUS tm 50 bp DNA circular UNK 15-OCT-2012
DEFINITION tm circular
ACCESSION tm
VERSION tm
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 acatccgaac ataaacaacc cacatacgat ttaggtgaca ctatagaacc
//
'''),)
)
raw.append(
('60meNXeGKO7ahZwcIl5yXHFC3Yg',
parse('''
>fw3
cacatacgatttaggtgacactatagaac
>rv
ggttgtttatgttcggatgtg
LOCUS tm 50 bp DNA circular UNK 15-OCT-2012
DEFINITION tm circular
ACCESSION tm
VERSION tm
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 ccacatccga acataaacaa cccacatacg atttaggtga cactatagaa
//
'''),)
)
raw.append(
('y6ohCJ4O+8Is012DItz4F4saxNo',
parse('''
>f_Eric_Ma
ARATGAGTCTTCTRACCGAGGTCG
>r_Eric_Ma
TGAAAAGACATCYTCAAGYYTCTG
>templ
AGCAAAAGCAGGTAGATATTGAAAAATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCGTCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTCTCTGCAGGGAAGAACACTGATCTCGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAGAATGCCTTAAATGGGAATGGAGACCCAAACAACATGGACAGGGCAGTCAAACTATACAGGAAGCTGAAAAGAGAGATAACATTCCATGGGGCTAAAGAGGTTGCACTCAGCTATTCAACCGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTAACCACAGAAGTAGCTTTTGGCCTGGTGTGTGCCACTTGTGAGCAGATTGCTGACTCACAGCATCGATCTCACAGACAGATGGTGACTACCACCAACCCACTAATCAGGCATGAAAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCTGGATCGAGTGAACAGGCAGCGGAAGCCATGGAGGTTGCTAGTCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCACCCTAGCTCCAGTGCCGGTCTGAAAGATGATCTTCTTGAAAATTTGCAGGCCTACCAGAAGCGGATGGGAGTGCAAATGCAGCGATTCAAGTGATCCTCTCGTTATTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCCTTTCTTCAAATGTATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAGTGCCTGAGTCTATGAGGGAAGAGTATCGGCAGGAACAGCAGAGTGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCTTGTTTCTACT
'''),)
)
for key, tst in enumerate(raw):
print key
print tst[1][0].name
print "pcr test", key
print
self.assertEqual(tst[0], seguid(pcr(tst[1:]).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
primersearch -seqall ../../rawdata/FSC770.1.fna -infile primers.txt -mismatchpercent 1 -stdout --auto -mismatchpercent 20 -scircular1
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)
YEp24PGK_bgl = YEp24PGK.cut(BglII).pop()
stuffer1, xks1_bam, stuffer2 = xks1_pcr_product.cut(BamHI)
YEp24PGK_XK = (YEp24PGK_bgl+xks1_bam.rc()).looped()
YEp24PGK_XK = YEp24PGK_XK.synced(YEp24PGK)
print "The sequence of YEp24PGK_XK was generated"
print "Seguid of YEp24PGK_XK is correct", YEp24PGK_XK.seguid() == "HRVpCEKWcFsKhw/W+25ednUfldI"
YEp24PGK_XK.write("YEp24PGK_XK.gb")
print '''
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)
YEp24PGK_bgl = YEp24PGK.cut(BglII).pop()
stuffer1, xks1_bam, stuffer2 = xks1_pcr_product.cut(BamHI)
YEp24PGK_XK = (YEp24PGK_bgl + xks1_bam.rc()).looped()
YEp24PGK_XK = YEp24PGK_XK.synced(YEp24PGK)
print "The sequence of YEp24PGK_XK was generated"
print "Seguid of YEp24PGK_XK is correct", YEp24PGK_XK.seguid(
) == "HRVpCEKWcFsKhw/W+25ednUfldI"
YEp24PGK_XK.write("YEp24PGK_XK.gb")
# p2 = pydna.read(">p2\ngtgctatcagatgatacagtcg", ds = False)
# ann = pydna.Anneal((p1, p2), template)
import pydna
a = pydna.Dseqrecord("atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg")
b = pydna.Dseqrecord(
"ccaaacccaccaggtaccttatgtaagtacttcaagtcgccagaagacttcttggtcaagttgcc"
)
c = pydna.Dseqrecord(
"tgtactggtgctgaaccttgtatcaagttgggtgttgacgccattgccccaggtggtcgtttcgtt"
)
primer_pairs = pydna.assembly_primers([a, b, c], circular=True)
p = []
for t, (f, r) in zip([a, b, c], primer_pairs):
p.append(pydna.pcr(f, r, t))
obj = pydna.Assembly(p)
# print(assemblyobj)
# @memorize("function")
# def times_two(n):
# return n*2
#
# @memorize("method")
# class Doubler(object):
# def __init__(self, n):
# self.n=n
# self.key=str(n)
# def result(self):
# return self.n*2
#
>621_ScTPI1tpr_PacI (35-mer)
taattaaTTTTAGTTTATGTATGTGTTTTTTGTAG''', ds=False)
#PDC1tp_ScTKL1_RPS19btp
# RPS19btp_ScRPE1_RPS19atp
# RPS19atp_ScRKI1tp_TPI1tp
# TPI1tp_CiGXF1_ENO2tp
from pYPK0_PDC1tp_ScTKL1_RPS19btp import pYPK0_PDC1tp_ScTKL1_RPS19btp as cas1
from pYPK0_RPS19btp_ScRPE1_RPS19atp import pYPK0_RPS19btp_ScRPE1_RPS19atp as cas2
from pYPK0_RPS19atp_ScRKI1_TPI1tp import pYPK0_RPS19atp_ScRKI1_TPI1tp as cas3
from pYPK0_TPI1tp_CiGXF1_ENO2tp import pYPK0_TPI1tp_CiGXF1_ENO2tp as cas4
cas1 = pcr( p167, p647, cas1)
cas2 = pcr( p648, p651, cas2)
cas3 = pcr( p538, p621, cas3)
cas4 = pcr( p419, p166, cas4)
pYPK0_E_Z, stuffer = pYPK0.cut((EcoRV, ZraI))
#print [cas1, cas2, cas3, cas4, pYPK0_E_Z]
a = Assembly([cas1, cas2, cas3, cas4, pYPK0_E_Z], limit = 61)
seq = a.circular_products[0]
print seq.small_fig()
seq=seq.synced("tcgcgcgtttcggtgatgacggtgaaaacctctg")