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_pth1():
q = BPread("read1.gb", "gb")
w = BPread("read2.gb", "gb")
e = BPread("read3.fasta", "fasta")
r = BPread("read4.fasta", "fasta")
q.format("gb")
w.format("gb")
a, b = BPparse("pth1.txt", "gb")
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_read_from_file():
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()[3314:3325] == '2micron 2\xc2\xb5'
assert x.features[13].qualifiers['label'][0] == '2micron 2\xc2\xb5'
assert str(a.seq).lower()==str(b.seq).lower()==str(c.seq).lower()==str(d.seq).lower()
def test_parse2(self):
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
seqs = parse('./RefDataBjorn.fas')
self.assertTrue( len(seqs) == 771 )
self.assertTrue( 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():
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()[3314:3325] == '2micron 2\xc2\xb5'
assert x.features[13].qualifiers['label'][0] == '2micron 2\xc2\xb5'
assert str(a.seq).lower() == str(b.seq).lower() == str(
c.seq).lower() == str(d.seq).lower()
def test_parse2(self):
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
seqs = parse('./RefDataBjorn.fas')
self.assertTrue(len(seqs) == 771)
self.assertTrue(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_pth1():
q = BPread("read1.gb", "gb")
w = BPread("read2.gb", "gb")
e = BPread("read3.fasta", "fasta")
r = BPread("read4.fasta", "fasta")
q.format("gb")
w.format("gb")
a, b = BPparse("pth1.txt", "gb")
x, y = parse("pth1.txt")
assert a.features[13].qualifiers['label'][0] == '2micron 2\xc2\xb5'
assert a.format("gb")[3270:3281] == '2micron 2\xc2\xb5'
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_pth1():
q = BPread("read1.gb", "gb")
w = BPread("read2.gb", "gb")
e = BPread("read3.fasta", "fasta")
r = BPread("read4.fasta", "fasta")
q.format("gb")
w.format("gb")
a, b = BPparse("pth1.txt", "gb")
x, y = parse("pth1.txt")
assert a.features[13].qualifiers['label'][0] == '2micron 2\xc2\xb5'
assert a.format("gb")[3270:3281] == '2micron 2\xc2\xb5'
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 main():
import docopt
try:
arguments = docopt.docopt(__doc__)
except docopt.DocoptExit as e:
print e.message
if arguments['--version']:
from ._version import get_versions
__version__ = get_versions()['version'][:5]
del get_versions
print "ypkpathway version:",__version__
if arguments['<path>']:
file_ = arguments['<path>']
try:
with open(file_, "rU") as f: text=f.read()
except IOError:
print arguments['<path>'], 'could not be opened!'
sys.exit(1)
print "Assembly started! (This might take a while...)"
pw = PathWay( pydna.parse( text ) )
pw.generate_files()
try:
os.makedirs('ypk_assembly')
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
for name, content in pw.files.items():
with codecs.open(os.path.join('ypk_assembly',name),'w', "utf8") as f:
f.write(content)
print "Assembly finished! files written to folder ypkpathway"
print "Genbank record KC562906 downloaded from NCBI\n"
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")
def test_read_from_unicode():
with open("pth1.txt", "rU") as f:
text = f.read()
assert type(text) == str
x, y = parse(text)
assert x.format()[3314:3325] == '2micron 2\xc2\xb5'
p578,
p468,
p467,
p567,
p568,
p775,
p778,
p342) = pydna.parse( u''' >577
gttctgatcctcgagcatcttaagaattc
>578
gttcttgtctcattgccacattcataagt
>468
gtcgaggaacgccaggttgcccact
>467
ATTTAAatcctgatgcgtttgtctgcacaga
>567
GTcggctgcaggtcactagtgag
>568
GTGCcatctgtgcagacaaacg
>775
gcggccgctgacTTAAAT
>778
ggtaaatccggatTAATTAA
>342
CCTTTTTACGGTTCCTGGCCT''', ds=False)
def add_line_block(s):
return u"\n".join( u"|{}".format(line) for line in s.splitlines())
def test_read_from_unicode():
with open("pth1.txt", "rU") as f: text = f.read()
x,y = parse( text )
assert x.format()[3270:3281] == '2micron 2\xc2\xb5'
def test_parse1(self):
''' 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'
]
self.assertEqual([str(s.seq) for s in result], correct)
self.assertEqual([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()
self.assertEqual(str(result.seq), str(read(input).seq))
correct = '''ATGACTGAATTCAAGGCCGGTTCTGCTAAGAAAGGTGCTACACTTTTCAAGACTAGATGTCTACAATGCCACACCGTGGAAAAGGGTGGCCCACATAAGGTTGGTCCAAACTTGCATGGTATCTTTGGCAGACACTCTGGTCAAGCTGAAGGGTATTCGTACACAGATGCCAATATCAAGAAAAACGTGTTGTGGGACGAAAATAACATGTCAGAGTACTTGACTAACCCAAAGAAATATATTCCTGGTACCAAGATGGCCTTTGGTGGGTTGAAGAAGGAAAAAGACAGAAACGACTTAATTACCTACTTGAAAAAAGCCTGTGAGTAA'''
self.assertEqual(str(result.seq), correct)
self.assertTrue(result.linear == True)
self.assertTrue(result.circular == False)
seqs = parse('./RefDataBjorn.fas')
self.assertEqual(len(seqs), 771)
self.assertEqual(list(set([len(a) for a in seqs])), [901])
pAG25 = read("./pAG25.gb")
self.assertTrue(pAG25.circular == True)
self.assertTrue(pAG25.linear == False)
pCAPs = read("./pCAPs.gb")
self.assertTrue(pCAPs.circular == True)
self.assertTrue(pCAPs.linear == False)
pUC19 = read("./pUC19.gb")
self.assertTrue(pUC19.circular == True)
self.assertTrue(pUC19.linear == False)
def test_read_from_unicode():
with open("pth1.txt", "rU") as f: text = f.read()
assert type(text) == str
x,y = parse( text )
assert x.format()[3314:3325] == '2micron 2\xc2\xb5'
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
print "Genbank record KC562906 downloaded from NCBI\n"
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")
# coding: utf-8
from pydna import parse, eq
new_primer = parse("/home/bjorn/Dropbox/wikidata/PrimersToBuy.wiki", ds=False)
primer = parse("/home/bjorn/Dropbox/wikidata/Primers.wiki", ds=False)
primer = primer[::-1]
old_primer = primer[:37 + 18]
primer = primer[37 + 18:]
new_primer_dict = dict((p.id, p) for p in new_primer)
primer_dict = dict((p.id, p) for p in primer)
old_primer_dict = dict((p.id, p) for p in old_primer)
assert str(primer_dict["509_mycGFPr"].seq) == "CTACTTGTACAGCTCGTCCA"
assert primer[0].id == "0_S1"
assert primer[1].id == "1_5CYC1clone"
assert primer[580].id == "580_GXF1_YPK_fwd"
fprimer = parse("/home/bjorn/Dropbox/wikidata/New10.wiki", ds=False)
fprimer = fprimer[::-1]
fold_primer = fprimer[:37 + 18]
fprimer = fprimer[37 + 18:]
print len(primer), len(fprimer)
for i in range(1, len(primer)):
if not eq(primer[i], fprimer[i]):
print i
print primer[i].id, fprimer[i].id
raw_input()
def test_parse1(self):
''' 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']
self.assertEqual( [str(s.seq) for s in result], correct )
self.assertEqual( [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()
self.assertEqual( str(result.seq) , str(read(input).seq) )
correct = '''ATGACTGAATTCAAGGCCGGTTCTGCTAAGAAAGGTGCTACACTTTTCAAGACTAGATGTCTACAATGCCACACCGTGGAAAAGGGTGGCCCACATAAGGTTGGTCCAAACTTGCATGGTATCTTTGGCAGACACTCTGGTCAAGCTGAAGGGTATTCGTACACAGATGCCAATATCAAGAAAAACGTGTTGTGGGACGAAAATAACATGTCAGAGTACTTGACTAACCCAAAGAAATATATTCCTGGTACCAAGATGGCCTTTGGTGGGTTGAAGAAGGAAAAAGACAGAAACGACTTAATTACCTACTTGAAAAAAGCCTGTGAGTAA'''
self.assertEqual( str(result.seq) , correct )
self.assertTrue( result.linear == True )
self.assertTrue( result.circular == False )
seqs = parse('./RefDataBjorn.fas')
self.assertEqual( len(seqs) , 771 )
self.assertEqual( list(set([len (a) for a in seqs])) ,[901])
pAG25 = read("./pAG25.gb")
self.assertTrue( pAG25.circular == True )
self.assertTrue( pAG25.linear == False)
pCAPs = read("./pCAPs.gb")
self.assertTrue( pCAPs.circular == True )
self.assertTrue( pCAPs.linear == False)
pUC19 = read("./pUC19.gb")
self.assertTrue( pUC19.circular == True )
self.assertTrue( pUC19.linear == False)
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"
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))
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from pydna import pcr, parse, Assembly
from Bio.Restriction import ZraI, AjiI, EcoRV
from pYPK0 import pYPK0
p167,p166 = parse('''>167_pCAPSfw (24-mer)
TCCTGACGGGTAATTTTGATTTGC
>166_pCAPSrv (24-mer)
CTGTGAAGTGGCTGAAATTTCGTA''')
p413,p625 = parse('''>413_ScPDC1tpf (24-mer)
TTAAATAAGGGTAGCCTCCCCATA
>625_ScPDC1tpr_PacI (34-mer)
taattaaTTTGATTGATTTGACTGTGTTATTTTG''', ds=False)
p648,p647 = parse('''>648_ScRPS19btpf2
ttaaatTCTAGTATGGTTTGAAACCT
>647_ScRPS19btpr_PacI
taattaaCTTTATTATCTTTGGTTCTAT''', ds=False)
#652
p538,p651 = parse('''>538_ScRPS19atpr_FspA (26-mer)
gcgcatGTTAACTGAAATGAAAATTT
>651_ScRPS19atpr_PacI
taattaaTTTTACTCTATTTGTCGATC''', ds=False)
p419,p621 = parse('''>419_ScTPI1tpf (32-mer)