def test_parse_error():
from pydna.parsers import parse
data = '''
LOCUS
DATA_IS_NOT_A_SEQUENCE
//'''
parse(data)
assert parse(data) == []
def test_misc_parse():
from pydna.parsers import parse
from Bio.SeqIO import read as BPread
from Bio.SeqIO import parse as BPparse
q = BPread("read1.gb", "gb")
w = BPread("read2.gb", "gb")
e = BPread("read3.fasta", "fasta")
r = BPread("read4.fasta", "fasta")
with open("pth1.txt", "r", encoding="utf-8") as f:
a, b = BPparse(f, "gb")
print("|" + a.features[13].qualifiers['label'][0] + "|")
print("|" + a.format("gb")[3314:3324] + "|")
assert a.features[13].qualifiers['label'][0] == '2micron 2µ'
assert a.format("gb")[3268:3278] == '2micron 2µ'
x, y = parse("pth1.txt")
assert "".join(a.format("gb").splitlines()[1:]) == "".join(
x.format("gb").splitlines()[1:])
assert "".join(b.format("gb").strip().splitlines()[4:]) == "".join(
y.format("gb").splitlines()[4:])
def test_ypk():
datafiles = '''pth1.txt|pYPK0_CiGXF1_PsXYL2.gb|iM8oDuvJPMPO995IdW3B0oo0Hkc
pth2.txt|pYPK0_SsXYL1_SsXYL2.gb|CB_qLhPgemW0XNLQOQEAdJKFujU
pth3.txt|pYPK0_NC_006038_CiGXF1_PsXYL2.gb|48_Bek9U1wxXlq1otmE7YHjYpnk
pth4.txt|pYPK0_SsXYL1_SsXYL2_ScXKS1.gb|5OxynmwQA3br0cKAG8It7VVNGrg
pth5.txt|pYPK0_SsXYL1_SsXYL2_ScXKS1_ScTAL1.gb|K8z4ijkYa0hA0KEOhv7-6PNJgBM
pth6.txt|pYPK0_SsXYL1_SsXYL2_ScXKS1_ScTAL1.gb|K8z4ijkYa0hA0KEOhv7-6PNJgBM
pth7.txt|pYPK0_SsXYL1_SsXYL2_ScXKS1_ScTAL1.gb|K8z4ijkYa0hA0KEOhv7-6PNJgBM'''
for pYPKa_A in (True, False):
for datafile in textwrap.dedent(datafiles).split():
file_, name, code = datafile.split("|")
print()
print("############################")
print("datafile = ", file_)
print("pYPKa_A = ", pYPKa_A)
print("############################")
with open(file_, "r",) as f: text = f.read()
try:
shutil.rmtree(tmp)
except OSError:
pass
pw = pathway( parse(text), tmp, pYPKa_A=pYPKa_A)
s = read( os.path.join(tmp, name) )
with open(code+".txt") as f: c = f.read()
assert "".join( x for x in c.lower() if not x.isspace()) == str(s.seq).lower()
def test_read_from_unicode():
from pydna.readers import read
from pydna.parsers import parse
with open("pth1.txt", "r", encoding="utf-8") as f:
text = f.read()
assert type(text) == str
x, y = parse(text)
assert x.format()[3268:3278] == '2micron 2µ'
def main():
try:
arguments = docopt.docopt(__doc__)
except docopt.DocoptExit as e:
#print(e)
sys.exit(0)
dir_ = "ypk_assembly"
if arguments["<dir>"]:
dir_= str(arguments["<dir>"])
if arguments["--no_pYPKa_A"]:
pYPKa_A = False
else:
pYPKa_A = True
if arguments["--version"]:
from ._version import get_versions
__version__ = get_versions()["version"][:5]
del get_versions
print("ypkpathway version:",__version__)
print(" pydna version:",pydna.__version__)
if arguments["<path>"]:
file_ = str(arguments["<path>"])
try:
with open(file_, "r") as f: text=f.read()
except IOError:
print(arguments["<path>"], "could not be opened!")
sys.exit(1)
#dir_ = os.path.splitext(os.path.basename(file_))[0]
dir_, ext = os.path.splitext(os.path.abspath(file_))
print("Assembly started! (This might take a while...)")
#print(file_)
#print(dir_)
#print(os.path.abspath(file_))
#print(os.path.abspath(dir_))
#print(os.path.splitext(os.path.abspath(file_)))
#print(os.path.basename(dir_))
#import sys;sys.exit(42)
fl, log = pathway( parse(text), dir_, pYPKa_A=pYPKa_A )
with open(os.path.join(dir_, "log.txt"),"w") as f: f.write(log)
filename = os.path.basename(file_)
shutil.copy2( filename, os.path.join(dir_, "INDATA_"+os.path.basename((dir_)+".txt")))
print("opening IPython notebook {}".format(fl.path))
subprocess.Popen(["jupyter", "notebook", os.path.join(dir_, "pw.ipynb")])
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 solveAssembly(self):
printline = self.qprintline
self.plainTextEdit_2.clear()
self.tabWidget.setCurrentIndex(1)
flbase = os.path.basename(str(self.filename))
title = 'Assembly log for ' + flbase
printline('='*len(title))
printline(title)
printline('='*len(title))
#print(type(self.plainTextEdit.toPlainText()))
#qstringobj = self.plainTextEdit.toPlainText().encode('utf-8')
#print(type(qstringobj)) #<class 'PyQt4.QtCore.QString'>
#print(qstringobj.toUtf8()[3268:3279])
#print(str(qstringobj.toUtf8()[3268:3279]))
#print(type(rawtext), "rawtext")
#codec0 = .QTextCodec.codecForName("UTF-16");
#rawtext = unicode(codec0.fromUnicode(tmp), 'UTF-16')
#unicode(qstringobj.toUtf8(), encoding="UTF-8").decode()
qstringobj = self.plainTextEdit.toPlainText()
#import sys;sys.exit(42)
pth = parse( qstringobj )
#import sys;sys.exit(42)
if len(pth)==0:
printline("No of sequences found in Data window")
return
if self.filename is None:
self.fileSaveAs()
dir_, ext = os.path.splitext( str(self.filename))
fl, log = ypkpathway.pathway( pth, dir_, pYPKa_A = not self.checkbox.isChecked(), print = printline)
if not fl:
return
with open(os.path.join(dir_, "log.txt"),"w") as f: f.write(log)
shutil.copy2( str(self.filename), os.path.join(dir_, "INDATA_"+os.path.basename(str(self.filename))))
printline('')
printline('\n\nAssembly finished.')
printline('click on the Open pathway button above to open the pathway in the default web browser')
self.nb = fl.path
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_parse2():
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from pydna.parsers import parse
from pydna.readers import read
seqs = parse('RefDataBjorn.fas')
assert len(seqs) == 771
assert list(set([len(a) for a in seqs])) == [901]
for i, s in enumerate(seqs):
a = s.description
b = a.split()
c = "|".join([b[0], b[1], b[3]])
s.id = b[2].replace(" ", "_") + "_" + str(i)
s.description = ""
if b[3] == "Zenion hololepis":
s.id = b[3].replace(" ", "_") + "_" + str(i)
s.seq.alphabet = IUPACAmbiguousDNA()
def test_read_from_file():
from pydna.readers import read
from pydna.parsers import parse
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()[3268:3278] == '2micron 2µ'
assert x.features[13].qualifiers['label'][0] == u'2micron 2µ'
assert str(a.seq).lower() == str(b.seq).lower() == str(
c.seq).lower() == str(d.seq).lower()
def test_parse1():
from pydna.parsers import parse
from pydna.readers import read
''' 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'
]
assert [str(s.seq) for s in result] == correct
assert [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()
assert str(result.seq) == str(read(input).seq)
correct = '''ATGACTGAATTCAAGGCCGGTTCTGCTAAGAAAGGTGCTACACTTTTCAAGACTAGATGTCTACAATGCCACACCGTGGAAAAGGGTGGCCCACATAAGGTTGGTCCAAACTTGCATGGTATCTTTGGCAGACACTCTGGTCAAGCTGAAGGGTATTCGTACACAGATGCCAATATCAAGAAAAACGTGTTGTGGGACGAAAATAACATGTCAGAGTACTTGACTAACCCAAAGAAATATATTCCTGGTACCAAGATGGCCTTTGGTGGGTTGAAGAAGGAAAAAGACAGAAACGACTTAATTACCTACTTGAAAAAAGCCTGTGAGTAA'''
assert str(result.seq) == correct
assert result.linear == True
assert result.circular == False
seqs = parse('RefDataBjorn.fas')
assert len(seqs) == 771
assert list(set([len(a) for a in seqs])) == [901]
pAG25 = read("pAG25.gb")
assert pAG25.circular == True
assert pAG25.linear == False
pCAPs = read("pCAPs.gb")
assert pCAPs.circular == True
assert pCAPs.linear == False
pUC19 = read("pUC19.gb")
assert pUC19.circular == True
assert pUC19.linear == False
input = '''
ID example standard; DNA; UNC; 3 BP.
SQ Sequence 3 BP;
aaa 3
//
'''
result = parse(input).pop()
input = '''
ID name? standard; circular DNA; UNK; 100 BP.
XX
DT 25-DEC-2017
XX
DE description?.
XX
AC id?;
XX
SV id?
XX
KW .
XX
OS .
OC .
OC .
XX
FH Key Location/Qualifiers
SQ Sequence 100 BP;
aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa 60
aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa 100
//
'''
result = parse(input).pop()
import pytest
from pydna.amplify import pcr
from pydna.assembly import Assembly
from pydna.dseqrecord import Dseqrecord
from pydna.design import primer_design
from pydna.design import assembly_fragments
from pydna.design import circular_assembly_fragments
from pydna.parsers import parse
from pydna.primer import Primer
frags = parse('''
>49
ccaaggacacaatcgagctccgatccgtactgtcgagaaacttgtatcc
>50
ctctaactagtatggatagccgtgtcttcactgtgctgcggctacccatc
>51
gtagtgaaacatacacgttgctcgggttcaccccggtccgttctgagtcga
''')
from Bio.Restriction import BamHI
bam = Dseqrecord(BamHI.site)
def test_primer_design_all_Dseqrecords():
with pytest.raises(ValueError):
assembly_fragments(frags, 20)
def test_primer_design_all_pcr_products():
x = [primer_design(f) for f in frags]
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_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)
