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_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_no_fwdprimer_anneal():
f0, r0 = parse_primers('''>ForwardPrimer
gctact
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = f0
r = r0
t = t0
with pytest.raises(ValueError):
pcr(f, r, t)
def test_pcr_not_specific():
f0, r0 = parse_primers(""">ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg""")
t0 = Dseqrecord(
"gctactacacacgtactgactgtgctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
)
f = f0
r = r0
t = t0
with pytest.raises(ValueError):
pcr(f, r, t)
def test_feature_note():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
t0.add_feature()
del t0.features[0].qualifiers["label"]
t0.features[0].qualifiers["note"] = ["note"]
f = f0
r = r0
t = t0
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
assert pcr(f, r, t).name == "note"
def test_Amplicon_argument():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = f0
r = r0
t = t0
ampl = pcr(f, r, t)
assert str(ampl.seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
amplicon_from_amplicon = pcr(ampl)
assert str(amplicon_from_amplicon.seq
) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_string_arguments():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = str(f0.seq)
r = str(r0.seq)
t = str(t0.seq)
assert str(pcr(
(f, r), t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_Primer_arguments():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = f0
r = r0
t = t0
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_Dseq_arguments():
from pydna.dseq import Dseq
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = Dseq(str(f0.seq))
r = Dseq(str(r0.seq))
t = Dseq(str(t0.seq))
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_feature_label():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
t0.add_feature()
f = f0
r = r0
t = t0
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_Seq_arguments():
from Bio.Seq import Seq
f0, r0 = parse_primers(""">ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg""")
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = Seq(str(f0.seq))
r = Seq(str(r0.seq))
t = Seq(str(t0.seq))
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_circ_pcr():
"""
<-----------------------------------------------------58->
<----------------------------33->
ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggcc
|||||||||||||||||||||||||
TCAGGTGAGGCGGAACCAACCCTCCTGGCCATGggaggggccgtggtggacgagggccccacaggcg-->
||||||||||||||||||||||||||
ggcggaaccaaccctcctggccATGgactacaaagacgatgacgacaagcttgcggc
<----------------------------------------------------------------------42->
<-----------------------------------------------------25-><------------17->
ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggcc
|||||||||||||||||||||||||
ggaggggccgtggtggacgagggccccacaggcgTCAGGTGAGGCGGAACCAACCCTCCTGGCCATG
||||||||||||||||||||||||||
ggcggaaccaaccctcctggccATGgactacaaagacgatgacgacaagcttgcggc
"""
s = parse(
"""
>MCT4_flaghis_rv
gccgcaagcttgtcgtcatcgtctttgtagtcCATggccaggagggttggttccgcc
>MCT4_flaghis_fw
ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggcc""",
ds=False,
)
t = parse("""
>hej circular
TCAGGTGAGGCGGAACCAACCCTCCTGGCCATGggaggggccgtggtggacgagggccccacaggcg
""")
p = pcr(s, t)
assert (
str(p.seq).lower() ==
"ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggccccacaggcgtcaggtgaggcggaaccaaccctcctggccatggactacaaagacgatgacgacaagcttgcggc"
)
def test_set_primer_footprint():
f, r = parse_primers(""">ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg""")
t = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
ampl = pcr((f, r), t)
assert len(ampl.forward_primer.footprint) == 22
assert len(ampl.reverse_primer.footprint) == 22
ampl.set_forward_primer_footprint(15)
ampl.set_reverse_primer_footprint(15)
assert len(ampl.forward_primer.footprint) == 15
assert len(ampl.reverse_primer.footprint) == 15
def test_circ_pcr():
'''
<-----------------------------------------------------58->
<----------------------------33->
ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggcc
|||||||||||||||||||||||||
TCAGGTGAGGCGGAACCAACCCTCCTGGCCATGggaggggccgtggtggacgagggccccacaggcg-->
||||||||||||||||||||||||||
ggcggaaccaaccctcctggccATGgactacaaagacgatgacgacaagcttgcggc
<----------------------------------------------------------------------42->
<-----------------------------------------------------25-><------------17->
ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggcc
|||||||||||||||||||||||||
ggaggggccgtggtggacgagggccccacaggcgTCAGGTGAGGCGGAACCAACCCTCCTGGCCATG
||||||||||||||||||||||||||
ggcggaaccaaccctcctggccATGgactacaaagacgatgacgacaagcttgcggc
'''
s = parse('''
>MCT4_flaghis_rv
gccgcaagcttgtcgtcatcgtctttgtagtcCATggccaggagggttggttccgcc
>MCT4_flaghis_fw
ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggcc''',
ds=False)
t = parse('''
>hej circular
TCAGGTGAGGCGGAACCAACCCTCCTGGCCATGggaggggccgtggtggacgagggccccacaggcg
''')
p = pcr(s, t)
assert str(p.seq).lower(
) == 'ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggccccacaggcgtcaggtgaggcggaaccaaccctcctggccatggactacaaagacgatgacgacaagcttgcggc'
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 pcr(template,*primers):
""" Forward PCR reaction w/ primers and template """
return amplify.pcr(primers,template)
pYPKa_Z = pYPKa.linearize(ZraI)
pYPKa_A = pYPKa.linearize(AjiI)
pYPKa_E = pYPKa.linearize(EcoRV)
bbdict = {"Z": pYPKa_Z, "A": pYPKa_A, "E": pYPKa_E}
fdict = {"Z": "promoter", "A": "gene", "E": "terminator"}
csvfile = "promoter_list_003.csv"
with open(csvfile) as csvfile:
reader = csv.reader(csvfile)
for row in reader:
ins, letter, pf, pr, template, comment = row
temp = genbank(template)
insert = pcr(p[int(pf)], p[int(pr)], temp)
label = f"{ins}_promoter"
if letter == "Z":
insert.add_feature(type="promoter",
name=label,
ApEinfo_label=label,
ApEinfo_fwdcolor="#FC6600",
ApEinfo_revcolor="#7C4700",
fp=p[int(pf)].format("tab").strip(),
rp=p[int(pr)].format("tab").strip(),
reference=template)
if letter == "E":
>567_pCAPsAjiIF (23-mer)
GTcggctgcaggtcactagtgag
>577_crp585-557 (29-mer)
gttctgatcctcgagcatcttaagaattc
>468_pCAPs_release_fw (25-mer)
gtcgaggaacgccaggttgcccact
>467_pCAPs_release_re (31-mer)
ATTTAAatcctgatgcgtttgtctgcacaga
>568_pCAPsAjiIR (22-mer)
GTGCcatctgtgcagacaaacg
>578_crp42-70 (29-mer)
gttcttgtctcattgccacattcataagt''')
p = pcr(p577, p567, pYPKa_Z_prom)
g = pcr(p468, p467, pYPKa_A_saat)
t = pcr(p568, p578, pYPKa_E_term)
pYPKpw = read("pYPKpw.gb")
from Bio.Restriction import ZraI
pYPKpw_lin = pYPKpw.linearize(ZraI)
asm = Assembly( (pYPKpw_lin, p, g, t) )
candidate = asm.circular_products[0]
def test_shifts():
from pydna.parsers import parse
from pydna.parsers import parse_primers
from pydna.amplify import pcr
#from pydna.amplify import nopcr
s = parse('''
>MCT4_flaghis_rv
gccgcaagcttgtcgtcatcgtctttgtagtcCATggccaggagggttggttccgcc
>MCT4_flaghis_fw
ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggcc''',
ds=False)
t = parse('''
>hej circular
TCAGGTGAGGCGGAACCAACCCTCCTGGCCATGggaggggccgtggtggacgagggccccacaggcg
''')
p = pcr(s, t)
assert str(p.seq).lower(
) == 'ccaccaccaccaccaccaccaccaccaccacggaggggccgtggtggacgagggccccacaggcgtcaggtgaggcggaaccaaccctcctggccatggactacaaagacgatgacgacaagcttgcggc'
f, r, t = parse('''
#A
>ForwardPrimer
actacacacgtactgactg
>ReversePrimer
ggttactgactctatcttg
>MyTemplate
gctactacacacgtactgactGcctcCaagatAgagtcagtaaccaca''')
a = pcr(f, r, t)
assert str(
a.seq).lower() == "actacacacgtactgactGcctcCaagatAgagtcagtaacc".lower()
f, r, t = parse('''
#B
>ForwardPrimer
actacacacgtactgactg
>ReversePrimer
ggttactgactctatcttg
>MyTemplate circular
gctactacacacgtactgactgcctccaagatagagtcagtaaccaca''')
# actacacacgtactgactg>
# |||||||||||||||||||
# gctactacacacgtactgactgcctccaagatagagtcagtaaccaca
#
# cgatgatgtgtgcatgactgacggaggttctatctcagtcattggtgt
# |||||||||||||||||||
# <gttctatctcagtcattgg
b = pcr(f, r, t)
assert a.seq == b.seq
a.template = None
b.template = None
assert a == b
f, r, t = parse('''
#C
>ForwardPrimer
actacacacgtactgactg
>ReversePrimer
ggttactgactctatcttg
>MyTemplate circular
cgtactgactgcctccaagatagagtcagtaaccacagctactacaca''')
c = pcr(f, r, t)
assert b.seq == c.seq
f, r, t = parse('''
#D
>ForwardPrimer
actacacacgtactgactg
>ReversePrimer
ggttactgactctatcttg
>MyTemplate48 circular
tccaagatagagtcagtaaccacagctactacacacgtactgactgcc''')
'''
012345678901234567890123456789012345678901234567
------------27--------------
actacacacgtactgactg
tccaagatagagtcagtaaccacagctactacacacgtactgactgcc
caagatagagtcagtaacc
--
012345678901234567890123456789012345678901234567
------------23----------
actacacacgtactgactg
actacacacgtactgactgcctccaagatagagtcagtaaccacagct
caagatagagtcagtaacc
------------------------------------------
actacacacgtactgactgcctccaagatagagtcagtaacc
'''
d = pcr(f, r, t)
assert c.seq == d.seq
f, r, t = parse('''
#E
>ForwardPrimer
actacacacgtactgactg
>ReversePrimer
ggttactgactctatcttg
>MyTemplate circular
gagtcagtaaccacagctactacacacgtactgactGcctccaagata''')
e = pcr(f, r, t)
assert d.seq == e.seq
f, r, t = parse('''
#F
>ForwardPrimer
actacacacgtactgactg
>ReversePrimer
ggttactgactctatcttg
>MyTemplate circular
actacacacgtactgactGcctccaagatagagtcagtaaccacagct''')
f = pcr(f, r, t)
def test_wrong_argument_type():
with pytest.raises(TypeError):
pcr(1, 2, 3)
print(insertname, pf, pr, comment)
fp = lp[int(pf)]
rp = lp[int(pr)]
gbref = p.promoter().description
gblink = p.cds().id
template = Dseqrecord(p.promoter())
templatesize = len(template)
insertseguid = template.seguid()
finalcseguidZ = (pYPKa.linearize(ZraI) +
pcr(fp, rp, template)).looped().cseguid()
finalcseguidE = (pYPKa.linearize(EcoRV) +
pcr(fp, rp, template)).looped().cseguid()
content = t.format(tp=insertname,
gbref=gbref,
gblink=gblink,
templatesize=templatesize,
insertseguid=insertseguid,
finalcseguidZ=finalcseguidZ,
finalcseguidE=finalcseguidE,
fpn=fp.name,
fps=fp.seq,
rpn=rp.name,
rps=rp.seq)
def test_pcr():
''' 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("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):
assert tst[0] == seguid(pcr(tst[1:]).seq)
