def test_primer_Design_given_both_primers():
b = Dseqrecord(
"agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
with pytest.raises(ValueError):
primer_design(b,
fp=Primer("agctactgactattag"),
rp=Primer("tagatcagtacagtca"))
def test_primer_Design_with_linker():
''' test_primer_design'''
b = Dseqrecord(
"agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord(
"tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
frags = assembly_fragments((primer_design(b), l, primer_design(c)))
asm1 = Assembly(frags)
assert asm1.assemble_linear()[0].seguid(), (
b + l + c).seguid() == 'l95igKB8iKAKrvvqE9CYksyNx40'
frags = assembly_fragments(
(primer_design(b), l, primer_design(c), primer_design(b)))
b2 = pcr(frags[-1].forward_primer, frags[0].reverse_primer, b)
asm2 = Assembly((b2, frags[1], frags[2]))
assert (b + l +
c).looped().cseguid() == asm2.assemble_circular()[0].cseguid()
assert (b + l + c).looped().cseguid() == 'jdHXfQI5k4Sk2ESiZYfKv4oP2FI'
def test_primer_design_same_first_and_third_Dseqrecord():
from pydna.dseqrecord import Dseqrecord
x = [primer_design(f) for f in frags]
y = assembly_fragments([frags[0], x[1], frags[0]], 20)
z = Assembly(y, limit=20)
result = z.assemble_circular()[0]
assert result.cseguid() == (frags[0] + frags[1]).looped().cseguid()
a = Dseqrecord("ccaaggacacaatcgagctccgatccgtactgtcgagaaacttgtatcc",
name="a")
b = Dseqrecord(
"ctgtcgagaaacttgtatccctctaactagtatggatagccgtgtcttcactgtgctgcggctacccatcccaaggacacaatcgagctc",
name="b",
)
z = Assembly((a, b, a), limit=20)
result = z.assemble_linear()[0]
assert (
str(result.seq) ==
"ccaaggacacaatcgagctccgatccgtactgtcgagaaacttgtatccctctaactagtatggatagccgtgtcttcactgtgctgcggctacccatcccaaggacacaatcgagctccgatccgtactgtcgagaaacttgtatcc"
)
result = z.assemble_circular()[0]
assert result.cseguid() == (frags[0] + frags[1]).looped().cseguid()
def test_primer_design_four_fragments():
x = [primer_design(f) for f in frags]
fourth = Dseqrecord("TAAAAATAAAATTGTTGACAGCAGAAGTGATATAGAAATTTGTTAATTATTA")
y = assembly_fragments(x + [fourth], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1] + frags[2] + fourth).seq
def test_primer_Design_multiple_products():
b = Dseqrecord(
"agctactgactattaggggttaagctactgactattaggggtttctgatcatctgatctactatctgactgtactgatcta"
)
from pydna import _PydnaWarning
with pytest.warns(_PydnaWarning):
a = primer_design(b)
def test_cut_feat():
from pydna.readers import read
from pydna.amplify import pcr
from pydna.design import primer_design
from pydna.dseqrecord import Dseqrecord
from Bio.Restriction import EcoRI
puc19 = read('pUC19_MarkBudde.gb')
assert len(puc19.features) == 19
puc_lin = puc19[:]
assert len(puc_lin.features) == 19
ampl = primer_design(puc_lin)
pf, pr = ampl.forward_primer, ampl.reverse_primer
pcrProd = pcr(pf, pr, puc19)
assert len(pcrProd.features) == 21
assert len(pcrProd.cut(EcoRI)[1].features) == 16
def amplicon_to_dseqrecord(a):
d = Dseqrecord(a.seq)
d.features = a.features
return d
pcrProdDseqrecord = amplicon_to_dseqrecord(pcrProd)
assert len(pcrProdDseqrecord.cut(EcoRI)[1].features) == 16
def test_circular_assembly_fragments2():
x = [primer_design(f) for f in frags]
y = circular_assembly_fragments((frags[0], x[1], x[2]), 20)
z = Assembly(y, limit=20)
result = z.assemble_circular()[0]
assert str(
result.seq
) == "ccaaggacacaatcgagctccgatccgtactgtcgagaaacttgtatccctctaactagtatggatagccgtgtcttcactgtgctgcggctacccatcgtagtgaaacatacacgttgctcgggttcaccccggtccgttctgagtcga"
def test_primer_Design():
''' test_primer_design'''
a = Dseqrecord(
"atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg")
b = Dseqrecord(
"ccaaacccaccaggtaccttatgtaagtacttcaagtcgccagaagacttcttggtcaagttgcc")
c = Dseqrecord(
"tgtactggtgctgaaccttgtatcaagttgggtgttgacgccattgccccaggtggtcgtttcgtt")
frags = assembly_fragments([primer_design(r) for r in (a, b, c)])
asm = Assembly(frags)
assert asm.assemble_linear()[0].seguid() == "1eNv3d_1PqDPP8qJZIVoA45Www8"
frags = assembly_fragments([primer_design(r) for r in (a, b, c, a)])
a2 = pcr(frags[-1].forward_primer, frags[0].reverse_primer, a)
asm = Assembly((a2, frags[1], frags[2]))
assert asm.assemble_circular()[0].cseguid(
) == "V3Mi8zilejgyoH833UbjJOtDMbc"
def build_primers_for_part(self, part):
"""Build extraction primers and assign them into the part."""
part_seq_record = part.get_sequence()
forward_primer = part.extraction_primers.forward_primer if part.has_primers else None
reverse_primer = part.extraction_primers.reverse_primer if part.has_primers else None
amplicon = primer_design(Dseqrecord(part_seq_record),
fp=forward_primer,
rp=reverse_primer,
tm_func=self._perform_tm_func,
limit=13)
if not part.has_primers:
part.set_extraction_primers(
PrimerPair.from_sequences(amplicon.forward_primer.seq,
amplicon.reverse_primer.seq))
return amplicon
from pydna.design import primer_design
from pydna.dseqrecord import Dseqrecord
t = Dseqrecord("atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg")
from pydna.primer import Primer
pf = Primer("atgactgctaacccttccttggtg")
print(pf.name)
ampl = primer_design(t, fp=pf)
print(ampl.forward_primer.name)
from pydna.genbank import genbank
from pydna.design import primer_design
from pydna.amplify import pcr
from pydna.readers import read
from pydna.parsers import parse_primers
from pydna.assembly import Assembly
from pydna.gel import Gel
###############################################################################
saat = genbank("AF193791 REGION: 78..1895")
saat_pcr_prod = primer_design(saat)
pYPKa=read("pYPKa.gb")
from Bio.Restriction import AjiI
pYPKa_AjiI = pYPKa.linearize(AjiI)
pYPKa_A_saat = ( pYPKa_AjiI + saat_pcr_prod ).looped()
pYPKa_Z_prom = read("pYPKa_Z_TEF1.gb")
pYPKa_E_term = read("pYPKa_E_TPI1.gb")
p567,p577,p468,p467,p568,p578 = parse_primers('''
>567_pCAPsAjiIF (23-mer)
GTcggctgcaggtcactagtgag
>577_crp585-557 (29-mer)
def test_primer_design_first_and_third_Dseqrecord():
x = [primer_design(f) for f in frags]
y = assembly_fragments([frags[0], x[1], frags[2]], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1] + frags[2]).seq
def test_primer_design_linker_first():
x = [primer_design(f) for f in frags]
y = assembly_fragments([bam, x[0], x[1], x[2]], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (bam + frags[0] + frags[1] + frags[2]).seq
def test_primer_design_linker_third(): #
x = [primer_design(f) for f in frags]
y = assembly_fragments([x[0], x[1], bam, x[2]], maxlink=6, overlap=20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1] + bam + frags[2]).seq
def test_primer_design_all_pcr_products():
x = [primer_design(f) for f in frags]
y = assembly_fragments(x, 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1] + frags[2]).seq
def test_primer_design_two_fragments():
x = [primer_design(f) for f in frags]
y = assembly_fragments([x[0], x[1]], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1]).seq
def test_primer_design_linker_second_before_Dseqrecord():
x = [primer_design(f) for f in frags]
y = assembly_fragments([x[0], bam, frags[1], x[2]], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + bam + frags[1] + frags[2]).seq
def test_primer_Design_given_rv_primer():
b = Dseqrecord(
"agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
a = primer_design(b, rp=Primer("tagatcagtacagtca"))
assert str(a.forward_primer.seq) == 'agctactgactattag' #g
def test_primer_Design_given_fw_primer():
b = Dseqrecord(
"agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
a = primer_design(b, fp=Primer("agctactgactattag"))
assert str(a.reverse_primer.seq) == 'tagatcagtacagtca'
def test_primer_design_two_fragments_linker_in_between(): #
x = [primer_design(f) for f in frags]
y = assembly_fragments([x[0], bam, x[1]], 20, 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + bam + frags[1]).seq
def test_primer_design_two_fragments_flanking_linkers():
x = [primer_design(f) for f in frags]
y = assembly_fragments([bam, x[0], x[1], bam], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (bam + frags[0] + frags[1] + bam).seq
def test_primer_design_one_fragment_flanking_linkers():
x = [primer_design(f) for f in frags]
y = assembly_fragments([bam, x[0], bam], 20)
assert y[0].seq == (bam + frags[0] + bam).seq
