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 __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 test_primer_Design_saving_to_text_file():
files_ = [dedent(x) for x in
('''\
>fw64 t-sequence
atgactgctaacccttc
>rv64 t-sequence
catcgtaagtttcgaac''',
'''\
>fw64 t-sequence
atgactgctaacccttcN
>rv64 t-sequence
catcgtaagtttcgaacN''',
'''\
>fw64 t-sequence
atgactgctaacccttcN''',
'''\
>fw64 t-sequence
atgactgctaacccttcN
>rv64 t-sequence
catcgtaagtttcgaac''',
'''\
>rv64 t-sequence
catcgtaagtttcgaacN''',
'''\
>rv64 t-sequence
catcgtaagtttcgaacN
>fw64 t-sequence
atgactgctaacccttc''',
'''\
>fw64 t-sequenceZ
atgactgctaacccttc
>rv64 t-sequenceZ
catcgtaagtttcgaac''',
'''\
>fw64 t-sequenceZ
atgactgctaacccttc
>rv64 t-sequenceZ
catcgtaagtttcgaac
>fw64 t-sequence
atgactgctaacccttc
>rv64 t-sequence
catcgtaagtttcgaac''',
'''\
>fw64x t-sequence
atgactgctaacccttc
>rv64x t-sequence
catcgtaagtttcgaac''',
'''\
>fw64x t-sequence
atgactgctaacccttc
>rv64x t-sequence
catcgtaagtttcgaac
>fw64 t-sequence
atgactgctaacccttc
>rv64 t-sequence
catcgtaagtttcgaac''',
)]
templ=Dseqrecord("atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg")
templ.accession = "t-sequence"
try:
os.remove("PRIMERS.TXT")
except OSError:
pass
pf, pr = cloning_primers(templ, path="PRIMERS.TXT")
assert os.path.isfile("PRIMERS.TXT")
with open("PRIMERS.TXT", "r") as f: text=f.read().strip()
assert text == files_[0]
with open("PRIMERS.TXT", "w") as f: text=f.write(files_[1])
pf, pr = cloning_primers(templ, path="PRIMERS.TXT")
with open("PRIMERS.TXT", "r") as f: text=f.read().strip()
assert text == files_[1]
with open("PRIMERS.TXT", "w") as f: text=f.write(files_[2])
pf, pr = cloning_primers(templ, path="PRIMERS.TXT")
with open("PRIMERS.TXT", "r") as f: text=f.read().strip()
assert text == files_[3]
with open("PRIMERS.TXT", "w") as f: text=f.write(files_[4])
pf, pr = cloning_primers(templ, path="PRIMERS.TXT")
with open("PRIMERS.TXT", "r") as f: text=f.read().strip()
assert text == files_[5]
with open("PRIMERS.TXT", "w") as f: text=f.write(files_[6])
pf, pr = cloning_primers(templ, path="PRIMERS.TXT")
with open("PRIMERS.TXT", "r") as f: text=f.read().strip()
assert text == files_[7]
with open("PRIMERS.TXT", "w") as f: text=f.write(files_[8])
pf, pr = cloning_primers(templ, path="PRIMERS.TXT")
with open("PRIMERS.TXT", "r") as f: text=f.read().strip()
assert text == files_[9]
with open("PRIMERS.TXT", "w") as f: text=f.write('')
pf, pr = cloning_primers(templ, path="PRIMERS.TXT")
f, r = parse("PRIMERS.TXT", ds=False)
assert f.description == "fw64 t-sequence"
assert r.description == "rv64 t-sequence"
