Source code for pytadbit.mapping.restriction_enzymes
"""
14 nov. 2014
Definition and mapping of restriction enymes
"""
from __future__ import print_function
from re import compile
from warnings import warn
from collections import OrderedDict
from scipy.stats import binom_test
from pytadbit.utils.file_handling import magic_open
try:
basestring
except NameError:
basestring = str
def iupac2regex(restring):
"""
Convert target sites with IUPAC nomenclature to regex pattern
"""
restring = restring.replace('R', '[AG]')
restring = restring.replace('Y', '[CT]')
restring = restring.replace('M', '[AC]')
restring = restring.replace('K', '[GT]')
restring = restring.replace('S', '[CG]')
restring = restring.replace('W', '[AT]')
restring = restring.replace('H', '[ACT]')
restring = restring.replace('B', '[CGT]')
restring = restring.replace('V', '[ACG]')
restring = restring.replace('D', '[AGT]')
restring = restring.replace('N', '[ATGC]')
return restring
def count_re_fragments(fnam):
frag_count = {}
fhandler = open(fnam)
line = next(fhandler)
while line.startswith('#'):
line = next(fhandler)
try:
while True:
_, cr1, _, _, _, rs1, _, cr2, _, _, _, rs2, _ = line.split('\t')
try:
frag_count[(cr1, rs1)] += 1
except KeyError:
frag_count[(cr1, rs1)] = 1
try:
frag_count[(cr2, rs2)] += 1
except KeyError:
frag_count[(cr2, rs2)] = 1
line = next(fhandler)
except StopIteration:
pass
fhandler.close()
return frag_count
def map_re_sites_nochunk(enzyme_name, genome_seq, verbose=False):
"""
map all restriction enzyme (RE) sites of a given enzyme in a genome.
Position of a RE site is defined as the genomic coordinate of the first
nucleotide after the first cut (genomic coordinate starts at 1).
In the case of HindIII the genomic coordinate is this one:
123456 789...
|
v
-----A|AGCT T--------------
-----T TCGA|A--------------
In this example the coordinate of the RE site would be 7.
:param enzyme_name: name of the enzyme to map (upper/lower case are
important)
:param genome_seq: a dictionary containing the genomic sequence by
chromosome
"""
warn('WARNING: not reviewed since multiple-cut branch, and the use of regexpinstead of index')
if isinstance(enzyme_name, basestring):
enzyme_names = [enzyme_name]
elif isinstance(enzyme_name, list):
enzyme_names = enzyme_name
enzymes = {}
for name in enzyme_names:
enzymes[name] = RESTRICTION_ENZYMES[name]
# we match the full cut-site but report the position after the cut site
# (third group of the regexp)
restring = ('%s') % ('|'.join(['(?<=%s(?=%s))' % tuple(enzymes[n].split('|'))
for n in enzymes]))
# IUPAC conventions
restring = iupac2regex(restring)
enz_pattern = compile(restring)
frags = {}
count = 0
for crm in genome_seq:
seq = genome_seq[crm]
frags[crm] = [1]
for match in enz_pattern.finditer(seq):
pos = match.end() + 1
frags[crm].append(pos)
count += 1
# at the end of last chunk we add the chromosome length
frags[crm].append(len(seq))
if verbose:
print('Found %d RE sites' % count)
return frags
[docs]def map_re_sites(enzyme_name, genome_seq, frag_chunk=100000, verbose=False):
"""
map all restriction enzyme (RE) sites of a given enzyme in a genome.
Position of a RE site is defined as the genomic coordinate of the first
nucleotide after the first cut (genomic coordinate starts at 1).
In the case of HindIII the genomic coordinate is this one:
123456 789...
|
v
-----A|AGCT T--------------
-----T TCGA|A--------------
In this example the coordinate of the RE site would be 7.
:param enzyme_name: name of the enzyme to map (upper/lower case are
important)
:param genome_seq: a dictionary containing the genomic sequence by
chromosome
:param 100000 frag_chunk: in order to optimize the search for nearby RE
sites, each chromosome is splitted into chunks.
"""
if isinstance(enzyme_name, basestring):
enzyme_names = [enzyme_name]
elif isinstance(enzyme_name, list):
enzyme_names = enzyme_name
enzymes = {}
for name in enzyme_names:
enzymes[name] = RESTRICTION_ENZYMES[name]
# we match the full cut-site but report the position after the cut site
# (third group of the regexp)
restring = ('%s') % ('|'.join(['(?<=%s(?=%s))' % tuple(enzymes[n].split('|'))
for n in enzymes]))
# IUPAC conventions
restring = iupac2regex(restring)
enz_pattern = compile(restring)
frags = {}
count = 0
for crm in genome_seq:
seq = genome_seq[crm]
frags[crm] = dict([(i, []) for i in range(int(len(seq) // frag_chunk + 1))])
frags[crm][0] = [1]
for match in enz_pattern.finditer(seq):
pos = match.end() + 1
frags[crm][pos // frag_chunk].append(pos)
count += 1
# at the end of last chunk we add the chromosome length
frags[crm][len(seq) // frag_chunk].append(len(seq))
# now we need to assign as first RE site of a fragment the last RE site
# of previsou fragment, and as last RE site, the first RE site of the
# next fragment.
for i in range(int(len(seq) // frag_chunk + 1)):
try:
try:
frags[crm][i].insert(0, frags[crm][i - 1][-2])
except IndexError:
# in case there was no RE site in previous fragment
frags[crm][i].insert(0, frags[crm][i - 1][-1])
except KeyError:
# it is the very first chunk
pass
plus = 1
while True:
try:
frags[crm][i].append(frags[crm][i + plus][0])
break
except IndexError:
# no RE site in this fragment, get "next RE site" from next
plus += 1
except KeyError:
# end of the chromosome
break
if verbose:
print('Found %d RE sites' % count)
return frags
def complementary(seq):
trs = dict([(nt1, nt2) for nt1, nt2 in zip('ATGCN', 'TACGN')])
return ''.join([trs[s] for s in seq[::-1]])
[docs]def repaired(r_enz):
"""
returns the resulting sequence after reparation of two digested and repaired
ends, marking dangling ends.
"""
site = RESTRICTION_ENZYMES[r_enz]
beg, end = site.split('|')
site = site.replace('|', '')
return complementary(beg + site[min(len(beg), len(end)) :
max(len(beg), len(end))])
def religateds(r_enzs):
"""
returns the resulting list of all possible sequences after religation of two
digested and repaired ends.
"""
ligations = OrderedDict()
for r_enz1 in r_enzs:
for r_enz2 in r_enzs:
site1 = RESTRICTION_ENZYMES[r_enz1]
site2 = RESTRICTION_ENZYMES[r_enz2]
beg1, end1 = site1.split('|')
_, end2 = site2.split('|')
site1 = site1.replace('|', '')
site2 = site2.replace('|', '')
ligations[(r_enz1, r_enz2)] = beg1 + end1[:len(end1)-len(beg1)] + end2
return ligations
def identify_re(fnam, nreads=100000):
"""
Search most probable restriction enzyme used in the Hi-C experiment.
Uses binomial test and some heuristics.
:param fnam: path to FASTQ file
:param 100000 nreads: number of reads to use for prediction, the more the
better (and slower)
:returns: 1- most probable pattern, 2- the corresponding list of restriction
enzyme names and 3- p-value of binomial test (which is not necessarily
meaningful).
"""
pats = {}
for k in RESTRICTION_ENZYMES:
pat = RESTRICTION_ENZYMES[k].split('|')[1]
if len(pat) < 1:
continue
pats.setdefault(pat, {'name': [], 're': compile(pat), 'count': 0})
pats[pat]['name'].append(k)
fh = magic_open(fnam)
for _ in range(nreads):
_ = next(fh)
s = next(fh)[:14]
_ = next(fh)
_ = next(fh)
for pat in pats:
m = pats[pat]['re'].match(s)
if m and m.start() == 0:
pats[pat]['count'] += 1
bestks = []
best_pv = 1
for pv, k in sorted((binom_test(pats[k]['count'], nreads, 0.25**len(k), alternative='greater'), k)
for k in pats if pats[k]['count'])[:20]:
if pv <= best_pv or pv < 1e-100:
if pv <= best_pv:
best_pv = pv
bestks.append(k)
# some times several patterns are equally probable (pv=0.0), in this case
# we take the longest pattern that has a unique length.
if len(bestks) > 1:
lens = [len(k) for k in bestks]
lens = dict((l, lens.count(l)) for l in set(lens))
bestk = max([k for k in bestks if lens[len(k)] == 1], key=len)
else:
bestk = bestks[0]
return bestk, pats[bestk]['name'], best_pv
class RE_dict(dict):
def __getitem__(self, i):
try:
return super(RE_dict, self).__getitem__(i)
except KeyError:
for nam in self:
if nam.lower() == i.lower():
return self[nam]
raise KeyError('Restriction Enzyme %s not found\n' % (i))
RESTRICTION_ENZYMES = RE_dict([('AanI' , 'TTA|TAA' ),
('AarI' , 'CACCTGC|' ),
('AasI' , 'GACNNNN|NNGTC' ),
('AatII' , 'GACGT|C' ),
('AbaSI' , 'C|' ),
('AbsI' , 'CC|TCGAGG' ),
('Acc16I' , 'TGC|GCA' ),
('Acc36I' , 'ACCTGC|' ),
('Acc65I' , 'G|GTACC' ),
('AccB1I' , 'G|GYRCC' ),
('AccB7I' , 'CCANNNN|NTGG' ),
('AccBSI' , 'CCG|CTC' ),
('AccI' , 'GT|MKAC' ),
('AccII' , 'CG|CG' ),
('AccIII' , 'T|CCGGA' ),
('AceIII' , 'CAGCTC|' ),
('AciI' , 'C|CGC' ),
('AclI' , 'AA|CGTT' ),
('AclWI' , 'GGATC|' ),
('AcoI' , 'Y|GGCCR' ),
('AcsI' , 'R|AATTY' ),
('AcuI' , 'CTGAAG|' ),
('AcvI' , 'CAC|GTG' ),
('AcyI' , 'GR|CGYC' ),
('AdeI' , 'CACNNN|GTG' ),
('AfaI' , 'GT|AC' ),
('AfeI' , 'AGC|GCT' ),
('AfiI' , 'CCNNNNN|NNGG' ),
('AflII' , 'C|TTAAG' ),
('AflIII' , 'A|CRYGT' ),
('AgeI' , 'A|CCGGT' ),
('AgsI' , 'TTS|AA' ),
('AhaIII' , 'TTT|AAA' ),
('AhdI' , 'GACNNN|NNGTC' ),
('AhlI' , 'A|CTAGT' ),
('AjiI' , 'CAC|GTC' ),
('AjnI' , '|CCWGG' ),
('AjuI' , 'GAANNNN|NNNTTGG' ),
('AleI' , 'CACNN|NNGTG' ),
('AlfI' , 'GC|ANNNNNNTGC' ),
('AloI' , 'GAACNN|NNNNTCC' ),
('AluBI' , 'AG|CT' ),
('AluI' , 'AG|CT' ),
('Alw21I' , 'GWGCW|C' ),
('Alw26I' , 'GTCTC|' ),
('Alw44I' , 'G|TGCAC' ),
('AlwFI' , 'GAAAYNNNNNRTG|GAAAYNNNNNRTG' ),
('AlwI' , 'GGATC|' ),
('AlwNI' , 'CAGNNN|CTG' ),
('Ama87I' , 'C|YCGRG' ),
('Aor13HI' , 'T|CCGGA' ),
('Aor51HI' , 'AGC|GCT' ),
('AoxI' , '|GGCC' ),
('ApaBI' , 'GCANNNNN|TGC' ),
('ApaI' , 'GGGCC|C' ),
('ApaLI' , 'G|TGCAC' ),
('ApeKI' , 'G|CWGC' ),
('ApoI' , 'R|AATTY' ),
('ApyPI' , 'ATCGAC|' ),
('AquII' , 'GCCGNAC|' ),
('AquIII' , 'GAGGAG|' ),
('AquIV' , 'GRGGAAG|' ),
('ArsI' , 'GACNN|NNNNTTYG' ),
('AscI' , 'GG|CGCGCC' ),
('AseI' , 'AT|TAAT' ),
('Asi256I' , 'G|ATC' ),
('AsiGI' , 'A|CCGGT' ),
('AsiSI' , 'GCGAT|CGC' ),
('Asp700I' , 'GAANN|NNTTC' ),
('Asp718I' , 'G|GTACC' ),
('AspA2I' , 'C|CTAGG' ),
('AspBHI' , 'YSCNS|' ),
('AspLEI' , 'GCG|C' ),
('AspS9I' , 'G|GNCC' ),
('AssI' , 'AGT|ACT' ),
('AsuC2I' , 'CC|SGG' ),
('AsuHPI' , 'GGTGA|' ),
('AsuI' , 'G|GNCC' ),
('AsuII' , 'TT|CGAA' ),
('AsuNHI' , 'G|CTAGC' ),
('AvaI' , 'C|YCGRG' ),
('AvaII' , 'G|GWCC' ),
('AvaIII' , 'ATGCAT|ATGCAT' ),
('AvrII' , 'C|CTAGG' ),
('AxyI' , 'CC|TNAGG' ),
('BaeGI' , 'GKGCM|C' ),
('BaeI' , 'A|CNNNNGTAYC' ),
('BalI' , 'TGG|CCA' ),
('BamHI' , 'G|GATCC' ),
('BanI' , 'G|GYRCC' ),
('BanII' , 'GRGCY|C' ),
('BarI' , 'GAAGNN|NNNNTAC' ),
('BasI' , 'CCANNNN|NTGG' ),
('BauI' , 'C|ACGAG' ),
('Bbr7I' , 'GAAGAC|' ),
('BbrPI' , 'CAC|GTG' ),
('BbsI' , 'GAAGAC|' ),
('Bbv12I' , 'GWGCW|C' ),
('BbvCI' , 'CC|TCAGC' ),
('BbvI' , 'GCAGC|' ),
('BbvII' , 'GAAGAC|' ),
('BccI' , 'CCATC|' ),
('Bce83I' , 'CTTGAG|' ),
('BceAI' , 'ACGGC|' ),
('BcefI' , 'ACGGC|' ),
('BcgI' , 'CG|ANNNNNNTGC' ),
('BciT130I' , 'CC|WGG' ),
('BciVI' , 'GTATCC|' ),
('BclI' , 'T|GATCA' ),
('BcnI' , 'CC|SGG' ),
('BcoDI' , 'GTCTC|' ),
('BcuI' , 'A|CTAGT' ),
('BdaI' , 'TG|ANNNNNNTCA' ),
('BetI' , 'W|CCGGW' ),
('BfaI' , 'C|TAG' ),
('BfiI' , 'ACTGGG|' ),
('BfmI' , 'C|TRYAG' ),
('BfoI' , 'RGCGC|Y' ),
('BfrI' , 'C|TTAAG' ),
('BfuAI' , 'ACCTGC|' ),
('BfuCI' , '|GATC' ),
('BfuI' , 'GTATCC|' ),
('BglI' , 'GCCNNNN|NGGC' ),
('BglII' , 'A|GATCT' ),
('BinI' , 'GGATC|' ),
('BisI' , 'GC|NGC' ),
('BlnI' , 'C|CTAGG' ),
('BlpI' , 'GC|TNAGC' ),
('BlsI' , 'GCN|GC' ),
('BmcAI' , 'AGT|ACT' ),
('Bme1390I' , 'CC|NGG' ),
('Bme18I' , 'G|GWCC' ),
('BmeDI' , 'C|' ),
('BmeRI' , 'GACNNN|NNGTC' ),
('BmeT110I' , 'C|YCGRG' ),
('BmgBI' , 'CAC|GTC' ),
('BmgI' , 'GKGCCC|GKGCCC' ),
('BmgT120I' , 'G|GNCC' ),
('BmiI' , 'GGN|NCC' ),
('BmrFI' , 'CC|NGG' ),
('BmrI' , 'ACTGGG|' ),
('BmsI' , 'GCATC|' ),
('BmtI' , 'GCTAG|C' ),
('BmuI' , 'ACTGGG|' ),
('BoxI' , 'GACNN|NNGTC' ),
('BpiI' , 'GAAGAC|' ),
('BplI' , 'GAG|NNNNNCTC' ),
('BpmI' , 'CTGGAG|' ),
('Bpu10I' , 'CC|TNAGC' ),
('Bpu1102I' , 'GC|TNAGC' ),
('Bpu14I' , 'TT|CGAA' ),
('BpuEI' , 'CTTGAG|' ),
('BpuMI' , 'CC|SGG' ),
('BpvUI' , 'CGAT|CG' ),
('Bsa29I' , 'AT|CGAT' ),
('BsaAI' , 'YAC|GTR' ),
('BsaBI' , 'GATNN|NNATC' ),
('BsaHI' , 'GR|CGYC' ),
('BsaI' , 'GGTCTC|' ),
('BsaJI' , 'C|CNNGG' ),
('BsaWI' , 'W|CCGGW' ),
('BsaXI' , 'AC|NNNNNCTCC' ),
('BsbI' , 'CAACAC|' ),
('Bsc4I' , 'CCNNNNN|NNGG' ),
('BscAI' , 'GCATC|' ),
('BscGI' , 'CCCGT|CCCGT' ),
('Bse118I' , 'R|CCGGY' ),
('Bse1I' , 'ACTGG|' ),
('Bse21I' , 'CC|TNAGG' ),
('Bse3DI' , 'GCAATG|' ),
('Bse8I' , 'GATNN|NNATC' ),
('BseAI' , 'T|CCGGA' ),
('BseBI' , 'CC|WGG' ),
('BseCI' , 'AT|CGAT' ),
('BseDI' , 'C|CNNGG' ),
('BseGI' , 'GGATG|' ),
('BseJI' , 'GATNN|NNATC' ),
('BseLI' , 'CCNNNNN|NNGG' ),
('BseMI' , 'GCAATG|' ),
('BseMII' , 'CTCAG|' ),
('BseNI' , 'ACTGG|' ),
('BsePI' , 'G|CGCGC' ),
('BseRI' , 'GAGGAG|' ),
('BseSI' , 'GKGCM|C' ),
('BseX3I' , 'C|GGCCG' ),
('BseXI' , 'GCAGC|' ),
('BseYI' , 'C|CCAGC' ),
('BsgI' , 'GTGCAG|' ),
('Bsh1236I' , 'CG|CG' ),
('Bsh1285I' , 'CGRY|CG' ),
('BshFI' , 'GG|CC' ),
('BshNI' , 'G|GYRCC' ),
('BshTI' , 'A|CCGGT' ),
('BshVI' , 'AT|CGAT' ),
('BsiEI' , 'CGRY|CG' ),
('BsiHKAI' , 'GWGCW|C' ),
('BsiHKCI' , 'C|YCGRG' ),
('BsiI' , 'C|ACGAG' ),
('BsiSI' , 'C|CGG' ),
('BsiWI' , 'C|GTACG' ),
('BsiYI' , 'CCNNNNN|NNGG' ),
('BslFI' , 'GGGAC|' ),
('BslI' , 'CCNNNNN|NNGG' ),
('BsmAI' , 'GTCTC|' ),
('BsmBI' , 'CGTCTC|' ),
('BsmFI' , 'GGGAC|' ),
('BsmI' , 'GAATGC|' ),
('BsnI' , 'GG|CC' ),
('Bso31I' , 'GGTCTC|' ),
('BsoBI' , 'C|YCGRG' ),
('Bsp119I' , 'TT|CGAA' ),
('Bsp120I' , 'G|GGCCC' ),
('Bsp1286I' , 'GDGCH|C' ),
('Bsp13I' , 'T|CCGGA' ),
('Bsp1407I' , 'T|GTACA' ),
('Bsp143I' , '|GATC' ),
('Bsp1720I' , 'GC|TNAGC' ),
('Bsp19I' , 'C|CATGG' ),
('Bsp24I' , 'GACN|NNNNNTGG' ),
('Bsp68I' , 'TCG|CGA' ),
('BspACI' , 'C|CGC' ),
('BspCNI' , 'CTCAG|' ),
('BspD6I' , 'GACTC|' ),
('BspDI' , 'AT|CGAT' ),
('BspEI' , 'T|CCGGA' ),
('BspFNI' , 'CG|CG' ),
('BspGI' , 'CTGGAC|CTGGAC' ),
('BspHI' , 'T|CATGA' ),
('BspLI' , 'GGN|NCC' ),
('BspLU11I' , 'A|CATGT' ),
('BspMI' , 'ACCTGC|' ),
('BspMII' , 'T|CCGGA' ),
('BspNCI' , 'CCAGA|CCAGA' ),
('BspOI' , 'GCTAG|C' ),
('BspPI' , 'GGATC|' ),
('BspQI' , 'GCTCTTC|' ),
('BspT104I' , 'TT|CGAA' ),
('BspT107I' , 'G|GYRCC' ),
('BspTI' , 'C|TTAAG' ),
('BsrBI' , 'CCG|CTC' ),
('BsrDI' , 'GCAATG|' ),
('BsrFI' , 'R|CCGGY' ),
('BsrGI' , 'T|GTACA' ),
('BsrI' , 'ACTGG|' ),
('BsrSI' , 'ACTGG|' ),
('BssAI' , 'R|CCGGY' ),
('BssECI' , 'C|CNNGG' ),
('BssHII' , 'G|CGCGC' ),
('BssKI' , '|CCNGG' ),
('BssMI' , '|GATC' ),
('BssNAI' , 'GTA|TAC' ),
('BssNI' , 'GR|CGYC' ),
('BssSI' , 'C|ACGAG' ),
('BssT1I' , 'C|CWWGG' ),
('Bst1107I' , 'GTA|TAC' ),
('Bst2BI' , 'C|ACGAG' ),
('Bst2UI' , 'CC|WGG' ),
('Bst4CI' , 'ACN|GT' ),
('Bst6I' , 'CTCTTC|' ),
('BstACI' , 'GR|CGYC' ),
('BstAFI' , 'C|TTAAG' ),
('BstAPI' , 'GCANNNN|NTGC' ),
('BstAUI' , 'T|GTACA' ),
('BstBAI' , 'YAC|GTR' ),
('BstBI' , 'TT|CGAA' ),
('BstC8I' , 'GCN|NGC' ),
('BstDEI' , 'C|TNAG' ),
('BstDSI' , 'C|CRYGG' ),
('BstEII' , 'G|GTNACC' ),
('BstENI' , 'CCTNN|NNNAGG' ),
('BstF5I' , 'GGATG|' ),
('BstFNI' , 'CG|CG' ),
('BstH2I' , 'RGCGC|Y' ),
('BstHHI' , 'GCG|C' ),
('BstKTI' , 'GAT|C' ),
('BstMAI' , 'GTCTC|' ),
('BstMBI' , '|GATC' ),
('BstMCI' , 'CGRY|CG' ),
('BstMWI' , 'GCNNNNN|NNGC' ),
('BstNI' , 'CC|WGG' ),
('BstNSI' , 'RCATG|Y' ),
('BstOI' , 'CC|WGG' ),
('BstPAI' , 'GACNN|NNGTC' ),
('BstPI' , 'G|GTNACC' ),
('BstSCI' , '|CCNGG' ),
('BstSFI' , 'C|TRYAG' ),
('BstSLI' , 'GKGCM|C' ),
('BstSNI' , 'TAC|GTA' ),
('BstUI' , 'CG|CG' ),
('BstV1I' , 'GCAGC|' ),
('BstV2I' , 'GAAGAC|' ),
('BstX2I' , 'R|GATCY' ),
('BstXI' , 'CCANNNNN|NTGG' ),
('BstYI' , 'R|GATCY' ),
('BstZ17I' , 'GTA|TAC' ),
('BstZI' , 'C|GGCCG' ),
('Bsu15I' , 'AT|CGAT' ),
('Bsu36I' , 'CC|TNAGG' ),
('BsuI' , 'GTATCC|' ),
('BsuRI' , 'GG|CC' ),
('BtgI' , 'C|CRYGG' ),
('BtgZI' , 'GCGATG|' ),
('BthCI' , 'GCNG|C' ),
('BtrI' , 'CAC|GTC' ),
('BtsCI' , 'GGATG|' ),
('BtsI' , 'GCAGTG|' ),
('BtsIMutI' , 'CAGTG|' ),
('BtuMI' , 'TCG|CGA' ),
('BveI' , 'ACCTGC|' ),
('Cac8I' , 'GCN|NGC' ),
('CaiI' , 'CAGNNN|CTG' ),
('CauII' , 'CC|SGG' ),
('CchII' , 'GGARGA|' ),
('CchIII' , 'CCCAAG|' ),
('CciI' , 'T|CATGA' ),
('CciNI' , 'GC|GGCCGC' ),
('Cdi630V' , 'CAAAAA|CAAAAA' ),
('CdiI' , 'CATC|G' ),
('CdpI' , 'GCGGAG|' ),
('CfoI' , 'GCG|C' ),
('Cfr10I' , 'R|CCGGY' ),
('Cfr13I' , 'G|GNCC' ),
('Cfr42I' , 'CCGC|GG' ),
('Cfr9I' , 'C|CCGGG' ),
('CfrI' , 'Y|GGCCR' ),
('Cgl13032I' , 'GGCGCA|GGCGCA' ),
('Cgl13032II' , 'ACGABGG|ACGABGG' ),
('ChaI' , 'GATC|' ),
('CjeFIII' , 'GCAAGG|GCAAGG' ),
('CjeFV' , 'GGRCA|GGRCA' ),
('CjeI' , 'CCA|NNNNNNGT' ),
('CjeNII' , 'GAGNNNNNGT|GAGNNNNNGT' ),
('CjeNIII' , 'GKAAYG|' ),
('CjeP659IV' , 'CACNNNNNNNGAA|CACNNNNNNNGAA' ),
('CjePI' , 'CCANN|NNNNNTC' ),
('CjuI' , 'CAYNNNNNRTG|CAYNNNNNRTG' ),
('CjuII' , 'CAYNNNNNCTC|CAYNNNNNCTC' ),
('ClaI' , 'AT|CGAT' ),
('CpoI' , 'CG|GWCCG' ),
('CseI' , 'GACGC|' ),
('CsiI' , 'A|CCWGGT' ),
('Csp6I' , 'G|TAC' ),
('CspAI' , 'A|CCGGT' ),
('CspCI' , 'C|AANNNNNGTGG' ),
('CspI' , 'CG|GWCCG' ),
('CstMI' , 'AAGGAG|' ),
('CviAII' , 'C|ATG' ),
('CviJI' , 'RG|CY' ),
('CviKI_1' , 'RG|CY' ),
('CviQI' , 'G|TAC' ),
('CviRI' , 'TG|CA' ),
('DdeI' , 'C|TNAG' ),
('DinI' , 'GGC|GCC' ),
('DpnI' , 'GA|TC' ),
('DpnII' , '|GATC' ),
('DraI' , 'TTT|AAA' ),
('DraII' , 'RG|GNCCY' ),
('DraIII' , 'CACNNN|GTG' ),
('DraRI' , 'CAAGNAC|' ),
('DrdI' , 'GACNNNN|NNGTC' ),
('DrdII' , 'GAACCA|GAACCA' ),
('DriI' , 'GACNNN|NNGTC' ),
('DsaI' , 'C|CRYGG' ),
('DseDI' , 'GACNNNN|NNGTC' ),
('EaeI' , 'Y|GGCCR' ),
('EagI' , 'C|GGCCG' ),
('Eam1104I' , 'CTCTTC|' ),
('Eam1105I' , 'GACNNN|NNGTC' ),
('EarI' , 'CTCTTC|' ),
('EciI' , 'GGCGGA|' ),
('Ecl136II' , 'GAG|CTC' ),
('EclXI' , 'C|GGCCG' ),
('Eco105I' , 'TAC|GTA' ),
('Eco130I' , 'C|CWWGG' ),
('Eco147I' , 'AGG|CCT' ),
('Eco24I' , 'GRGCY|C' ),
('Eco31I' , 'GGTCTC|' ),
('Eco32I' , 'GAT|ATC' ),
('Eco47I' , 'G|GWCC' ),
('Eco47III' , 'AGC|GCT' ),
('Eco52I' , 'C|GGCCG' ),
('Eco53kI' , 'GAG|CTC' ),
('Eco57I' , 'CTGAAG|' ),
('Eco57MI' , 'CTGRAG|' ),
('Eco72I' , 'CAC|GTG' ),
('Eco81I' , 'CC|TNAGG' ),
('Eco88I' , 'C|YCGRG' ),
('Eco91I' , 'G|GTNACC' ),
('EcoHI' , '|CCSGG' ),
('EcoICRI' , 'GAG|CTC' ),
('EcoNI' , 'CCTNN|NNNAGG' ),
('EcoO109I' , 'RG|GNCCY' ),
('EcoO65I' , 'G|GTNACC' ),
('EcoRI' , 'G|AATTC' ),
('EcoRII' , '|CCWGG' ),
('EcoRV' , 'GAT|ATC' ),
('EcoT14I' , 'C|CWWGG' ),
('EcoT22I' , 'ATGCA|T' ),
('EcoT38I' , 'GRGCY|C' ),
('EgeI' , 'GGC|GCC' ),
('EheI' , 'GGC|GCC' ),
('ErhI' , 'C|CWWGG' ),
('EsaBC3I' , 'TC|GA' ),
('EsaSSI' , 'GACCAC|GACCAC' ),
('Esp3I' , 'CGTCTC|' ),
('EspI' , 'GC|TNAGC' ),
('FaeI' , 'CATG|' ),
('FaiI' , 'YA|TR' ),
('FalI' , 'AAG|NNNNNCTT' ),
('FaqI' , 'GGGAC|' ),
('FatI' , '|CATG' ),
('FauI' , 'CCCGC|' ),
('FauNDI' , 'CA|TATG' ),
('FbaI' , 'T|GATCA' ),
('FblI' , 'GT|MKAC' ),
('FinI' , 'GGGAC|GGGAC' ),
('FmuI' , 'GGNC|C' ),
('Fnu4HI' , 'GC|NGC' ),
('FnuDII' , 'CG|CG' ),
('FokI' , 'GGATG|' ),
('FriOI' , 'GRGCY|C' ),
('FseI' , 'GGCCGG|CC' ),
('Fsp4HI' , 'GC|NGC' ),
('FspAI' , 'RTGC|GCAY' ),
('FspBI' , 'C|TAG' ),
('FspEI' , 'CC|' ),
('FspI' , 'TGC|GCA' ),
('GauT27I' , 'CGCGCAGG|CGCGCAGG' ),
('GdiII' , 'C|GGCCR' ),
('GlaI' , 'GC|GC' ),
('GluI' , 'GC|NGC' ),
('GsaI' , 'CCCAG|C' ),
('GsuI' , 'CTGGAG|' ),
('HaeI' , 'WGG|CCW' ),
('HaeII' , 'RGCGC|Y' ),
('HaeIII' , 'GG|CC' ),
('HapII' , 'C|CGG' ),
('HauII' , 'TGGCCA|' ),
('HgaI' , 'GACGC|' ),
('HgiAI' , 'GWGCW|C' ),
('HgiCI' , 'G|GYRCC' ),
('HgiEII' , 'ACCNNNNNNGGT|ACCNNNNNNGGT' ),
('HgiJII' , 'GRGCY|C' ),
('HhaI' , 'GCG|C' ),
('Hin1I' , 'GR|CGYC' ),
('Hin1II' , 'CATG|' ),
('Hin4I' , 'GAY|NNNNNVTC' ),
('Hin4II' , 'CCTTC|' ),
('Hin6I' , 'G|CGC' ),
('HinP1I' , 'G|CGC' ),
('HincII' , 'GTY|RAC' ),
('HindII' , 'GTY|RAC' ),
('HindIII' , 'A|AGCTT' ),
('HinfI' , 'G|ANTC' ),
('HpaI' , 'GTT|AAC' ),
('HpaII' , 'C|CGG' ),
('HphI' , 'GGTGA|' ),
('Hpy166II' , 'GTN|NAC' ),
('Hpy178III' , 'TC|NNGA' ),
('Hpy188I' , 'TCN|GA' ),
('Hpy188III' , 'TC|NNGA' ),
('Hpy8I' , 'GTN|NAC' ),
('Hpy99I' , 'CGWCG|' ),
('Hpy99XIII' , 'GCCTA|GCCTA' ),
('Hpy99XIV' , 'GGWTAA|GGWTAA' ),
('HpyAV' , 'CCTTC|' ),
('HpyCH4III' , 'ACN|GT' ),
('HpyCH4IV' , 'A|CGT' ),
('HpyCH4V' , 'TG|CA' ),
('HpyF10VI' , 'GCNNNNN|NNGC' ),
('HpyF3I' , 'C|TNAG' ),
('HpySE526I' , 'A|CGT' ),
('Hsp92I' , 'GR|CGYC' ),
('Hsp92II' , 'CATG|' ),
('HspAI' , 'G|CGC' ),
('Jma19592I' , 'GTATNAC|GTATNAC' ),
('KasI' , 'G|GCGCC' ),
('KflI' , 'GG|GWCCC' ),
('Kpn2I' , 'T|CCGGA' ),
('KpnI' , 'GGTAC|C' ),
('KroI' , 'G|CCGGC' ),
('Ksp22I' , 'T|GATCA' ),
('Ksp632I' , 'CTCTTC|' ),
('KspAI' , 'GTT|AAC' ),
('KspI' , 'CCGC|GG' ),
('Kzo9I' , '|GATC' ),
('LguI' , 'GCTCTTC|' ),
('LpnI' , 'RGC|GCY' ),
('LpnPI' , 'CCDG|' ),
('Lsp1109I' , 'GCAGC|' ),
('LweI' , 'GCATC|' ),
('MabI' , 'A|CCWGGT' ),
('MaeI' , 'C|TAG' ),
('MaeII' , 'A|CGT' ),
('MaeIII' , '|GTNAC' ),
('MalI' , 'GA|TC' ),
('MaqI' , 'CRTTGAC|' ),
('MauBI' , 'CG|CGCGCG' ),
('MbiI' , 'CCG|CTC' ),
('MboI' , '|GATC' ),
('MboII' , 'GAAGA|' ),
('McaTI' , 'GCGC|GC' ),
('McrI' , 'CGRY|CG' ),
('MfeI' , 'C|AATTG' ),
('MflI' , 'R|GATCY' ),
('MhlI' , 'GDGCH|C' ),
('MjaIV' , 'GTNNAC|GTNNAC' ),
('MkaDII' , 'GAGAYGT|GAGAYGT' ),
('MlsI' , 'TGG|CCA' ),
('MluCI' , '|AATT' ),
('MluI' , 'A|CGCGT' ),
('MluNI' , 'TGG|CCA' ),
('Mly113I' , 'GG|CGCC' ),
('MlyI' , 'GAGTC|' ),
('MmeI' , 'TCCRAC|' ),
('MnlI' , 'CCTC|' ),
('Mph1103I' , 'ATGCA|T' ),
('MreI' , 'CG|CCGGCG' ),
('MroI' , 'T|CCGGA' ),
('MroNI' , 'G|CCGGC' ),
('MroXI' , 'GAANN|NNTTC' ),
('MscI' , 'TGG|CCA' ),
('MseI' , 'T|TAA' ),
('MslI' , 'CAYNN|NNRTG' ),
('Msp20I' , 'TGG|CCA' ),
('MspA1I' , 'CMG|CKG' ),
('MspCI' , 'C|TTAAG' ),
('MspI' , 'C|CGG' ),
('MspJI' , 'CNNR|' ),
('MspR9I' , 'CC|NGG' ),
('MssI' , 'GTTT|AAAC' ),
('MstI' , 'TGC|GCA' ),
('MunI' , 'C|AATTG' ),
('Mva1269I' , 'GAATGC|' ),
('MvaI' , 'CC|WGG' ),
('MvnI' , 'CG|CG' ),
('MvrI' , 'CGAT|CG' ),
('MwoI' , 'GCNNNNN|NNGC' ),
('NaeI' , 'GCC|GGC' ),
('NarI' , 'GG|CGCC' ),
('NciI' , 'CC|SGG' ),
('NcoI' , 'C|CATGG' ),
('NdeI' , 'CA|TATG' ),
('NdeII' , '|GATC' ),
('NgoAVIII' , '|GACNNNNNTGA' ),
('NgoMIV' , 'G|CCGGC' ),
('NhaXI' , 'CAAGRAG|CAAGRAG' ),
('NheI' , 'G|CTAGC' ),
('NlaCI' , 'CATCAC|' ),
('NlaIII' , 'CATG|' ),
('NlaIV' , 'GGN|NCC' ),
('Nli3877I' , 'CYCGR|G' ),
('NmeAIII' , 'GCCGAG|' ),
('NmeDI' , '|RCCGGY' ),
('NmuCI' , '|GTSAC' ),
('NotI' , 'GC|GGCCGC' ),
('NruI' , 'TCG|CGA' ),
('NsbI' , 'TGC|GCA' ),
('NsiI' , 'ATGCA|T' ),
('NspBII' , 'CMG|CKG' ),
('NspI' , 'RCATG|Y' ),
('NspV' , 'TT|CGAA' ),
('OliI' , 'CACNN|NNGTG' ),
('PabI' , 'GTA|C' ),
('PacI' , 'TTAAT|TAA' ),
('PaeI' , 'GCATG|C' ),
('PaeR7I' , 'C|TCGAG' ),
('PagI' , 'T|CATGA' ),
('PalAI' , 'GG|CGCGCC' ),
('PasI' , 'CC|CWGGG' ),
('PauI' , 'G|CGCGC' ),
('PceI' , 'AGG|CCT' ),
('PciI' , 'A|CATGT' ),
('PciSI' , 'GCTCTTC|' ),
('PcsI' , 'WCGNNNN|NNNCGW' ),
('PctI' , 'GAATGC|' ),
('PdiI' , 'GCC|GGC' ),
('PdmI' , 'GAANN|NNTTC' ),
('PenI' , 'GCAGT|GCAGT' ),
('PfeI' , 'G|AWTC' ),
('Pfl1108I' , 'TCGTAG|TCGTAG' ),
('Pfl23II' , 'C|GTACG' ),
('PflFI' , 'GACN|NNGTC' ),
('PflMI' , 'CCANNNN|NTGG' ),
('PfoI' , 'T|CCNGGA' ),
('PinAI' , 'A|CCGGT' ),
('PlaDI' , 'CATCAG|' ),
('Ple19I' , 'CGAT|CG' ),
('PleI' , 'GAGTC|' ),
('PluTI' , 'GGCGC|C' ),
('PmaCI' , 'CAC|GTG' ),
('PmeI' , 'GTTT|AAAC' ),
('PmlI' , 'CAC|GTG' ),
('PpiI' , 'GAACN|NNNNCTC' ),
('PpsI' , 'GAGTC|' ),
('Ppu10I' , 'A|TGCAT' ),
('Ppu21I' , 'YAC|GTR' ),
('PpuMI' , 'RG|GWCCY' ),
('PscI' , 'A|CATGT' ),
('PshAI' , 'GACNN|NNGTC' ),
('PshBI' , 'AT|TAAT' ),
('PsiI' , 'TTA|TAA' ),
('Psp03I' , 'GGWC|C' ),
('Psp124BI' , 'GAGCT|C' ),
('Psp1406I' , 'AA|CGTT' ),
('Psp5II' , 'RG|GWCCY' ),
('Psp6I' , '|CCWGG' ),
('PspCI' , 'CAC|GTG' ),
('PspEI' , 'G|GTNACC' ),
('PspGI' , '|CCWGG' ),
('PspLI' , 'C|GTACG' ),
('PspN4I' , 'GGN|NCC' ),
('PspOMI' , 'G|GGCCC' ),
('PspOMII' , 'CGCCCAR|' ),
('PspPI' , 'G|GNCC' ),
('PspPPI' , 'RG|GWCCY' ),
('PspPRI' , 'CCYCAG|' ),
('PspXI' , 'VC|TCGAGB' ),
('PsrI' , 'GAACNN|NNNNTAC' ),
('PssI' , 'RGGNC|CY' ),
('PstI' , 'CTGCA|G' ),
('PstNI' , 'CAGNNN|CTG' ),
('PsuI' , 'R|GATCY' ),
('PsyI' , 'GACN|NNGTC' ),
('PteI' , 'G|CGCGC' ),
('PvuI' , 'CGAT|CG' ),
('PvuII' , 'CAG|CTG' ),
('R2_BceSIV' , '|GCAGC' ),
('RceI' , 'CATCGAC|' ),
('RdeGBI' , 'CCGCAG|CCGCAG' ),
('RdeGBII' , 'ACCCAG|' ),
('RdeGBIII' , '|TGRYCA' ),
('RflFIII' , 'CGCCAG|CGCCAG' ),
('RgaI' , 'GCGAT|CGC' ),
('RigI' , 'GGCCGG|CC' ),
('RlaI' , 'VCW|VCW' ),
('RleAI' , 'CCCACA|' ),
('RpaB5I' , 'CGRGGAC|' ),
('RpaBI' , 'CCCGCAG|' ),
('RpaI' , 'GTYGGAG|' ),
('RpaTI' , 'GRTGGAG|GRTGGAG' ),
('RruI' , 'TCG|CGA' ),
('RsaI' , 'GT|AC' ),
('RsaNI' , 'G|TAC' ),
('RseI' , 'CAYNN|NNRTG' ),
('Rsr2I' , 'CG|GWCCG' ),
('RsrII' , 'CG|GWCCG' ),
('SacI' , 'GAGCT|C' ),
('SacII' , 'CCGC|GG' ),
('SalI' , 'G|TCGAC' ),
('SanDI' , 'GG|GWCCC' ),
('SapI' , 'GCTCTTC|' ),
('SaqAI' , 'T|TAA' ),
('SatI' , 'GC|NGC' ),
('Sau3AI' , '|GATC' ),
('Sau96I' , 'G|GNCC' ),
('SauI' , 'CC|TNAGG' ),
('SbfI' , 'CCTGCA|GG' ),
('ScaI' , 'AGT|ACT' ),
('SchI' , 'GAGTC|' ),
('SciI' , 'CTC|GAG' ),
('ScrFI' , 'CC|NGG' ),
('SdaI' , 'CCTGCA|GG' ),
('SdeAI' , 'CAGRAG|' ),
('SdeOSI' , '|GACNNNNRTGA' ),
('SduI' , 'GDGCH|C' ),
('SecI' , 'C|CNNGG' ),
('SelI' , '|CGCG' ),
('SetI' , 'ASST|' ),
('SexAI' , 'A|CCWGGT' ),
('SfaAI' , 'GCGAT|CGC' ),
('SfaNI' , 'GCATC|' ),
('SfcI' , 'C|TRYAG' ),
('SfeI' , 'C|TRYAG' ),
('SfiI' , 'GGCCNNNN|NGGCC' ),
('SfoI' , 'GGC|GCC' ),
('Sfr274I' , 'C|TCGAG' ),
('Sfr303I' , 'CCGC|GG' ),
('SfuI' , 'TT|CGAA' ),
('SgeI' , 'CNNG|' ),
('SgfI' , 'GCGAT|CGC' ),
('SgrAI' , 'CR|CCGGYG' ),
('SgrBI' , 'CCGC|GG' ),
('SgrDI' , 'CG|TCGACG' ),
('SgrTI' , 'CCDS|' ),
('SgsI' , 'GG|CGCGCC' ),
('SimI' , 'GG|GTC' ),
('SlaI' , 'C|TCGAG' ),
('SmaI' , 'CCC|GGG' ),
('SmiI' , 'ATTT|AAAT' ),
('SmiMI' , 'CAYNN|NNRTG' ),
('SmlI' , 'C|TYRAG' ),
('SmoI' , 'C|TYRAG' ),
('SnaBI' , 'TAC|GTA' ),
('SnaI' , 'GTATAC|GTATAC' ),
('Sno506I' , 'GGCCGAG|GGCCGAG' ),
('SpeI' , 'A|CTAGT' ),
('SphI' , 'GCATG|C' ),
('SplI' , 'C|GTACG' ),
('SpoDI' , 'GCGGRAG|GCGGRAG' ),
('SrfI' , 'GCCC|GGGC' ),
('Sse232I' , 'CG|CCGGCG' ),
('Sse8387I' , 'CCTGCA|GG' ),
('Sse8647I' , 'AG|GWCCT' ),
('Sse9I' , '|AATT' ),
('SseBI' , 'AGG|CCT' ),
('SsiI' , 'C|CGC' ),
('SspD5I' , 'GGTGA|' ),
('SspDI' , 'G|GCGCC' ),
('SspI' , 'AAT|ATT' ),
('SstE37I' , 'CGAAGAC|' ),
('SstI' , 'GAGCT|C' ),
('Sth132I' , 'CCCG|' ),
('Sth302II' , 'CC|GG' ),
('StrI' , 'C|TCGAG' ),
('StsI' , 'GGATG|' ),
('StuI' , 'AGG|CCT' ),
('StyD4I' , '|CCNGG' ),
('StyI' , 'C|CWWGG' ),
('SwaI' , 'ATTT|AAAT' ),
('TaaI' , 'ACN|GT' ),
('TaiI' , 'ACGT|' ),
('TaqI' , 'T|CGA' ),
('TaqII' , 'GACCGA|' ),
('TasI' , '|AATT' ),
('TatI' , 'W|GTACW' ),
('TauI' , 'GCSG|C' ),
('TfiI' , 'G|AWTC' ),
('Tru1I' , 'T|TAA' ),
('Tru9I' , 'T|TAA' ),
('TscAI' , 'CASTG|' ),
('TseFI' , '|GTSAC' ),
('TseI' , 'G|CWGC' ),
('TsoI' , 'TARCCA|' ),
('Tsp45I' , '|GTSAC' ),
('Tsp4CI' , 'ACN|GT' ),
('TspDTI' , 'ATGAA|' ),
('TspEI' , '|AATT' ),
('TspGWI' , 'ACGGA|' ),
('TspMI' , 'C|CCGGG' ),
('TspRI' , 'CASTG|' ),
('TssI' , 'GAGNNNCTC|GAGNNNCTC' ),
('TstI' , 'CACN|NNNNNTCC' ),
('TsuI' , 'GCGAC|GCGAC' ),
('Tth111I' , 'GACN|NNGTC' ),
('Tth111II' , 'CAARCA|' ),
('UbaF11I' , 'TCGTA|TCGTA' ),
('UbaF12I' , 'CTACNNNGTC|CTACNNNGTC' ),
('UbaF13I' , 'GAGNNNNNNCTGG|GAGNNNNNNCTGG' ),
('UbaF14I' , 'CCANNNNNTCG|CCANNNNNTCG' ),
('UbaF9I' , 'TACNNNNNRTGT|TACNNNNNRTGT' ),
('UbaPI' , 'CGAACG|CGAACG' ),
('UcoMSI' , '|GAGCTC' ),
('UnbI' , '|GGNCC' ),
('Van91I' , 'CCANNNN|NTGG' ),
('Vha464I' , 'C|TTAAG' ),
('VneI' , 'G|TGCAC' ),
('VpaK11AI' , '|GGWCC' ),
('VpaK11BI' , 'G|GWCC' ),
('VspI' , 'AT|TAAT' ),
('WviI' , 'CACRAG|' ),
('XagI' , 'CCTNN|NNNAGG' ),
('XapI' , 'R|AATTY' ),
('XbaI' , 'T|CTAGA' ),
('XceI' , 'RCATG|Y' ),
('XcmI' , 'CCANNNNN|NNNNTGG' ),
('XhoI' , 'C|TCGAG' ),
('XhoII' , 'R|GATCY' ),
('XmaI' , 'C|CCGGG' ),
('XmaIII' , 'C|GGCCG' ),
('XmaJI' , 'C|CTAGG' ),
('XmiI' , 'GT|MKAC' ),
('XmnI' , 'GAANN|NNTTC' ),
('XspI' , 'C|TAG' ),
('YkrI' , 'C|' ),
('ZraI' , 'GAC|GTC' ),
('ZrmI' , 'AGT|ACT' ),
('Zsp2I' , 'ATGCA|T' )])
