def _check_effect_of_enzyme(self, seq_target, enzyme_name_list):
''' http://biopython.org/DIST/docs/cookbook/Restriction.html
biopython <= 1.76 for IUPACAmbiguousDNA()
'''
caps_ResTyp_dict = dict()
caps_check_dict = dict()
enzyme_map_txt = ""
# 4.1 Setting up an Analysis
# 4.2 Full restriction analysis
multi_site_seq = Seq(seq_target, IUPACAmbiguousDNA())
rb = Restriction.RestrictionBatch(enzyme_name_list)
Analong = Restriction.Analysis(rb, multi_site_seq)
# 4.5 Fancier restriction analysis
#
# full()
# all the enzymes in the RestrictionBatch
# {KpnI: [], EcoRV: [], EcoRI: [33]}
# with_sites()
# output only the result for enzymes which have a site
# result_dict = {EcoRI: [33]}
caps_ResTyp_dict = Analong.with_sites()
# make dictionary as string enzyme name
for enzyme_RestrictionType in caps_ResTyp_dict.keys():
enzyme_string = str(enzyme_RestrictionType)
# caps_check_dict
caps_check_dict[enzyme_string] = {
'ResType': enzyme_RestrictionType,
'res_list': caps_ResTyp_dict[enzyme_RestrictionType],
}
# detail information: make a restriction map of a sequence
if glv.conf.analyse_caps == True:
Analong.print_as('map')
enzyme_map_txt_all = Analong.format_output()
enzyme_map_txt = ""
for line in enzyme_map_txt_all.split('\n'):
if " Enzymes which " in line:
break
enzyme_map_txt += "{}\n".format(line)
enzyme_map_txt += "caps_check_dict={}".format(caps_check_dict)
return caps_check_dict, \
enzyme_map_txt
def main(argv: list) -> None:
if len(argv) < 2:
print('Please specify the input fasta file.')
exit(1)
### Prepare for the analysis
amb = IUPACAmbiguousDNA()
seq_ids = []
sites_results = []
output = dict()
### Read the fasta file
### Each fasta sequence should have a fasta description
for seq_item in SeqIO.parse(argv[1], 'fasta', alphabet=amb):
seq_ids.append(seq_item.id)
ana = Restriction.Analysis(Restriction.AllEnzymes,
seq_item.seq,
linear=True)
sites_results.append(ana.full())
for enzyme in Restriction.AllEnzymes:
sites = [r[enzyme] for r in sites_results]
nub_sites = [len(s) for s in sites]
### Check if the number of sites are the same
if nub_sites.count(nub_sites[0]) != len(nub_sites):
output[str(enzyme)] = nub_sites
print_fmt = '{:>15}' * (len(seq_ids) + 1)
print(print_fmt.format('Enzyme Name', *seq_ids))
for k, v in sorted(output.items()):
print(print_fmt.format(k, *v))
def restrict_function(in_IUPAC):
rb = Restriction.RestrictionBatch([], [
"C", "B", "E", "I", "K", "J", "M", "O", "N", "Q", "S", "R", "V",
"Y", "X"
])
return
def find_cuts(sequence, enzymes, linear=True):
batch = Restriction.RestrictionBatch(enzymes)
return [
cut
for cuts in batch.search(sequence, linear=linear).values()
for cut in cuts
]
def command(args):
"""
Lists the available restriction enzimes
"""
# selects the REs to list
if args.sup is not None:
res = r.RestrictionBatch(first=[], suppliers=args.sup)
elif args.all:
res = r.AllEnzymes
else:
res = r.CommOnly
# sorts the RE list
res = sorted(res, key=str)
for re in res:
sys.stdout.write("{:16} {}\n".format(str(re), re.site))
"""
if re_list is not None:
res = list(filter(lambda re: str(re) in re_list, res))
if re_suppliers is not None:
res = list(filter(lambda re: len(set(re.suppl) & re_suppliers), res))
return res
"""
sys.stdout.write("------\n{} restriction enzimes listed\n\n".format(len(res)))
def get_caps_result(cls, seq_target, enzyme_list):
# http://biopython.org/DIST/docs/cookbook/Restriction.html
# 2.6 Analysing sequences with a RestrictionBatch
# 20201130
#ar_seq = Seq(seq_target, IUPACAmbiguousDNA())
ar_seq = Seq(seq_target)
rb = Restriction.RestrictionBatch(enzyme_list)
# If linear is False, the restriction sites that span over
# the boundaries will be included.
caps_result_dict = rb.search(ar_seq, linear=True)
caps_result_dict_str = dict()
# log.debug("caps_result_dict {}".format(caps_result_dict))
# convert enzyme class from RestrictionType to string
for enzyme_RestrictionType in caps_result_dict.keys():
enzyme_string = str(enzyme_RestrictionType)
caps_result_dict_str[enzyme_string] = \
caps_result_dict[enzyme_RestrictionType]
# log.debug("{}".format(type(enzyme_RestrictionType)))
# log.debug("{}".format(str(enzyme_RestrictionType)))
# log.debug("{}".format(type(str(enzyme_RestrictionType))))
# sys.exit(1)
# log.debug("{} {}".format(caps_result_dict, caps_result_dict_str))
return caps_result_dict, caps_result_dict_str
def annotate_digestion_bands(record, enzymes, ladder):
linear = record.linear if hasattr(record, 'linear') else False
batch = Restriction.RestrictionBatch(enzymes)
cuts_dict = batch.search(record.seq)
all_cuts = sorted(
set([0, len(record)] + [c for cc in cuts_dict.values() for c in cc]))
bands = list(zip(all_cuts, all_cuts[1:]))
if (not linear) and len(bands) > 1:
start, end = bands.pop()
band0 = [-(end - start), bands[0][1]]
if bands == []:
bands = [band0]
else:
bands[0] = band0
sorted_bands = sorted(bands, key=lambda b: b[0] - b[1])
new_record = deepcopy(record)
for (band, label) in zip(sorted_bands, "abcdefghijkl"):
band_size = abs(band[1] - band[0])
formatted_size = bw.Band._format_dna_size(band_size)
annotate_record(new_record,
location=band,
label="%s - %s" % (label, formatted_size),
feature_type="misc_feature",
band_label=label,
band_size=band_size)
return new_record
def rebasecuts(Enzyme, Strand):
batch = Restriction.RestrictionBatch()
batch.add(Enzyme)
enzyme = batch.get(Enzyme)
Sites = enzyme.search(Strand)
return Sites
def check_restriction(seq, batch_list, to_print = True):
Ana = Restriction.Analysis(batch_list, seq, linear=False)
Ana.full()
num_cutting = len(Ana.with_sites())
if to_print:
Ana.print_as("map")
Ana.print_that()
return num_cutting
def number_enzyme(record):
my_batch = Restriction.RestrictionBatch(first=[], suppliers="N")
A = my_batch.search(record.seq, linear=False)
B = collections.OrderedDict(sorted(A.items(), key=lambda t: len(t[1])))
KK = []
for v in B.values():
KK.append(len(v))
return (KK)
def _look_for_site(site, re_name, should_match=False):
dna = Seq(site + str(self.test_dna), IUPAC.unambiguous_dna)
proc_dna = seq_opt.remove_restriction_sites(
dna,
self.codon_use_table,
Restriction.RestrictionBatch(
[Restriction.AllEnzymes.get(re_name)]),
)
assert (dna == proc_dna) == should_match
def number_enzyme2(record):
my_batch = Restriction.RestrictionBatch(first=[], suppliers="N")
A = my_batch.search(record.seq, linear=False)
B = collections.OrderedDict(sorted(A.items(), key=lambda t: len(t[1])))
print(len(B))
C = []
for k in B.keys():
C.append(k)
return (C)
def filter_re_sites(candidates): rb = Restriction.RestrictionBatch(restriction_enzymes) filtered_candidates = [] for c in candidates: rbsearch = rb.search(c['seqrec'].seq) matched = any([match for re in rbsearch.keys() for match in rbsearch[re]]) if not matched: filtered_candidates.append(c) return filtered_candidates
def fragmentSeq(seq: SeqRecord, rb: RestrictionBatch, ren: str) -> str:
sid = seq.id
slen = len(seq.seq)
print(f'Running insilico digest on {sid} of length {slen}')
# Running an analysis on this sequence
analysis = res.Analysis(rb, seq.seq)
# locations of cut sites for this particular restriction enzyme
resites = analysis.full()[ren]
def digest(fasta_records, enzyme):
"""
Divide a genome into restriction fragments. Support Arima-HiC enzyme cocktail
which digest chromatin at ^GATC and G^ANTC.
Parameters
----------
fasta_records : OrderedDict
Dictionary of chromosome names to sequence records.
enzyme: str
Name of restriction enzyme.
Returns
-------
Dataframe with columns: 'chrom', 'start', 'end'.
"""
import Bio.Restriction as biorst
import Bio.Seq as bioseq
# http://biopython.org/DIST/docs/cookbook/Restriction.html#mozTocId447698
chroms = fasta_records.keys()
try:
if enzyme.lower() == 'arima':
cocktail = biorst.RestrictionBatch(['MboI', 'HinfI'])
cut_finder = cocktail.search
else:
cut_finder = getattr(biorst, enzyme).search
except AttributeError:
raise ValueError('Unknown enzyme name: {}'.format(enzyme))
def _each(chrom):
seq = bioseq.Seq(str(fasta_records[chrom]))
tmp = cut_finder(seq)
if type(tmp) == list:
cut_sites = tmp
elif type(tmp) == dict:
cut_sites = []
for e in tmp:
cut_sites.extend(tmp[e])
cut_sites.sort()
cuts = np.r_[0, np.array(cut_sites) + 1, len(seq)].astype(int)
n_frags = len(cuts) - 1
frags = pd.DataFrame(
{
'chrom': [chrom] * n_frags,
'start': cuts[:-1],
'end': cuts[1:]
},
columns=['chrom', 'start', 'end'])
return frags
return pd.concat(map(_each, chroms), axis=0, ignore_index=True)
def changerestrictionsites(seqrecords, codons, revcodons):
"""uses remove site function to change restriction enzyme sites depending on location"""
for seqrecord in seqrecords:
rb = Restriction.RestrictionBatch([
Restriction.AscI, Restriction.BspQI, Restriction.PstI,
Restriction.EcoRI, Restriction.NotI, Restriction.BtsI,
Restriction.BsaI
])
reanalysis = rb.search(seqrecord.seq)
for key in reanalysis:
for _ in reanalysis[key]:
seqkey = Seq(key.site, generic_dna)
removesite(seqrecord, seqkey, codons, revcodons)
return seqrecords
def _restriction_count(self, sequence):
"""
Return the count per restriction enzyme that can bind in a certain
sequence.
@arg sequence: The sequence to be analysed
@type sequence: str
@return: A mapping of restriction enzymes to counts.
@rtype: dict
"""
analysis = Restriction.Analysis(self._restriction_batch, sequence)
return dict(
(unicode(k), len(v)) for k, v in analysis.with_sites().items())
def restriction_digest():
if session.username == None:
redirect(URL(r=request, f='../account/log_in'))
form = FORM(TABLE(TR("Sequence: ",
TEXTAREA(_type="text",
_value="Enter your DNA sequence in plain form",
_name="sequence",
requires=IS_NOT_EMPTY())),
TR("DNA Type: ",
SELECT("Linear", "Circular",
_name="dna_type")),
TR("Show Fragments: ",
SELECT("No", "Yes",
_name="show_frag")),
TR("", INPUT(_type="submit", _value="Digest DNA"))))
if form.accepts(request.vars,session):
from Bio import Restriction as R
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
if request.vars.dna_type == 'Linear':
dna_type = 'True'
else:
dna_type = 'False'
seq = Seq(request.vars.sequence, IUPAC.unambiguous_dna)
results = {}
nocut = []
results['sequence'] = seq
for enzyme in R.RestrictionBatch([], suppliers = ['F', 'N', 'R']):
digest = enzyme.search(seq, linear=dna_type)
digest.sort()
#fragment = [digest[x+1] - digest[x]
# for x in range(len(digest) - 1)]
#fragment.sort()
d = {}
if len(digest) == 0:
nocut.append(str(enzyme))
else:
d['Restriction site'] = enzyme.site
if dna_type == 'True':
d['Number of fragments'] = str(len(digest) + 1)
else:
d['Number of fragments'] = str(len(digest))
if request.vars.show_frag == 'Yes':
d['Cut positions'] = str(digest)
results[str(enzyme)] = d
results['Enzymes that do not cut'] = nocut
session['result'] = results
redirect(URL(r=request, f='restriction_digest_output'))
return dict(form=form)
def check_restriction(seq, batch_list, to_print=False):
"""
checks, using biopython, if the restriction enzymes specified cut the given sequence.
:param seq: the given dna sequence
:param batch_list: the RestrictionBatch object containing the restriction enzymes
:param to_print: True or false, to print to the screen the analysis results
:return: a dictionary containing what enzymes cut the sequence and where
"""
Ana = Restriction.Analysis(batch_list, seq, linear=False)
Ana.full()
cutting = Ana.with_sites()
if to_print:
Ana.print_as("map")
Ana.print_that()
return cutting
def RestrictionEnzymes(restriction_enzymes):
"""Create a RestrictionBatch instance to search for sites for a supplied
list of restriction enzymes.
Args:
restriction_enzymes (list[str], optional): List of restriction
enzymes to consider. Defaults to ["NdeI", "XhoI", "HpaI", "PstI",
"EcoRV", "NcoI", "BamHI"].
Returns:
Bio.Restriction.Restriction.RestrictionBatch: RestrictionBatch instance
configured with the input restriction enzymes.
"""
return Restriction.RestrictionBatch(
[Restriction.AllEnzymes.get(enz) for enz in restriction_enzymes])
def main():
rb_supp = Restriction.RestrictionBatch(
first=[],
suppliers=[
'C','B','E','I','K','J','M',\
'O','N','Q','S','R','V','Y','X'])
enz_cnt = len(rb_supp)
'''
>>> RestrictionBatch.show_codes() # as of May 2016 REBASE release.
C = Minotech Biotechnology
B = Life Technologies
E = Agilent Technologies
I = SibEnzyme Ltd.
K = Takara Bio Inc.
J = Nippon Gene Co., Ltd.
M = Roche Applied Science
O = Toyobo Biochemicals
N = New England Biolabs
Q = Molecular Biology Resources - CHIMERx
S = Sigma Chemical Corporation
R = Promega Corporation
V = Vivantis Technologies
Y = SinaClon BioScience Co.
X = EURx Ltd.
>>> # You can now choose a code and built your RestrictionBatch
'''
enzyme_list = list()
for enz_cls in rb_supp:
enzyme_list.append("{}\t{}\t{}\t{}".format(enz_cls, enz_cls.site,
enz_cls.elucidate(),
len(enz_cls)))
last_first_char = ""
line = ""
for enz_line in sorted(enzyme_list):
first_char = enz_line[0:1].upper()
if last_first_char != first_char:
print("\n#")
print(enz_line)
last_first_char = first_char
print("{}".format(enz_cnt), file=sys.stderr)
def getrestrictionmatches(seq, starting, enz):
from Bio import Restriction
rb = Restriction.RestrictionBatch(enz)
from Bio import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
amb = IUPACAmbiguousDNA()
s = Seq.Seq(seq, amb)
dic = rb.search(s)
hits = []
sites = []
for k, v in dic.items():
if len(v) > 0:
if max(v) >= starting:
hits.append(k)
sites.append(max(v))
return (hits, sites)
def __init__(self, orig, output):
"""
Initialise the instance with the original sequence.
@arg orig: The original sequence before mutation.
@type orig: Bio.Seq.Seq
@arg output: The output object.
@type output: mutalyzer.Output.Output
"""
self._shifts = defaultdict(int)
self._removed_sites = set()
self._restriction_batch = Restriction.RestrictionBatch([], ['N'])
self._output = output
self.orig = orig
# Note that we don't need to create a copy here, since mutation
# operations are not in place (`self._mutate`).
self.mutated = orig
def warnRestrictionSites(sequence,name,sites):
sites = sites.split(",")
rb = Restriction.RestrictionBatch(sites)
#Get Bio.Seq object
amb = IUPACAmbiguousDNA()
tmpSeq = Seq(sequence,amb)
#Search for sites
res = rb.search(tmpSeq)
#Sum hits
totalSites = 0
for v in res.values():
totalSites += len(v)
if totalSites > 0:
print >>sys.stderr, "Warning: The following positions in '%s' will be masked from tiles due to incompatible restictions sites:" % (name)
pp(res)
else:
pass
def hasRestrictionSites(sequence,sites):
#Parse sites
sites = sites.split(",")
rb = Restriction.RestrictionBatch(sites)
#Get Bio.Seq object
amb = IUPACAmbiguousDNA()
tmpSeq = Seq(sequence,amb)
#Search for sites
res = rb.search(tmpSeq)
#Sum hits
totalSites = 0
for v in res.values():
totalSites += len(v)
if totalSites > 0:
return True
else:
return False
def find_restriction_sites(fasta_file, enzyme_list: list) -> dict:
"""
Find the restriction sites of one or several enzyme in a sequence.
"""
# Create Restriction enzyme object
enzymes = Restriction.RestrictionBatch(enzyme_list)
# Load fasta file
seq_data = SeqIO.parse(fasta_file, "fasta")
restrict_dict = {}
for record in seq_data:
rest_sites_dict = enzymes.search(record.seq)
pos = []
for enz in enzymes:
pos.extend(rest_sites_dict[enz])
restrict_dict[record.id] = [
len(record.seq), list(np.unique(sorted(pos)))
]
return restrict_dict
def command(args):
"""
Lists all suppliers
"""
r.RestrictionBatch().show_codes()
def write_a_file(out_file):
my_batch = Restriction.RestrictionBatch(first=[], suppliers="N")
my_batch.search(record.seq)
f = open(out_file, 'w')
def get_restriction_enzymes(restriction_enzymes=_restriction_enzymes):
return Restriction.RestrictionBatch([
getattr(Restriction, enz) for enz in restriction_enzymes
if hasattr(Restriction, enz)
])
def predict_sequence_digestions(
sequence, enzymes, linear=True, max_enzymes_per_digestion=1
):
"""Return a dict giving bands sizes pattern for all possible digestions.
The digestions, double-digestions, etc. are listed and for each the
sequence band sizes are computed.
The result if of the form ``{digestion: {'cuts': [], 'bands': []}}``
Where ``digestion`` is a tuple of enzyme names e.g. ``('EcoRI', 'XbaI')``,
'cuts' is a list of cuts locations, 'bands' is a list of bands sizes
Parameters
----------
sequence
The sequence to be digested
enzymes
List of all enzymes to be considered
max_enzymes_per_digestion
Maximum number of enzymes allowed in one digestion
bands_to_migration
Function associating a migration distance to a band size. If provided,
each digestion will have a ``'migration'`` field (list of migration
distances) in addition to 'cuts' and 'bands'.
"""
restriction_batch = Restriction.RestrictionBatch(enzymes)
cuts_dict = restriction_batch.search(Seq(sequence))
def get_cuts(enzyme_name):
return {"cuts": cuts_dict[Restriction.__dict__[enzyme_name]]}
def _merge_digestions(digestion1, digestion2, sequence_length, linear):
"""Merge and sort the cuts from two different digestions."""
all_cuts = sorted(list(set(digestion1["cuts"] + digestion2["cuts"])))
return {
"cuts": all_cuts,
"bands": _compute_bands_from_cuts(
cuts=all_cuts, sequence_length=sequence_length, linear=linear
),
}
empty_digestion = ((), {"cuts": [], "bands": [len(sequence)]})
digestions_dict = OrderedDict([empty_digestion])
for n_enzymes in range(max_enzymes_per_digestion):
sub_enzymes = [
enzs for enzs in digestions_dict.keys() if len(enzs) == n_enzymes
]
for enzyme in enzymes:
sub_sub_enzymes = [
enzs for enzs in sub_enzymes if enzyme not in enzs
]
for enzs in sub_sub_enzymes:
digestion = tuple(sorted(enzs + (enzyme,)))
if digestion not in digestions_dict:
no_enzyme_band = len(get_cuts(enzyme)["cuts"]) == 0
no_enzs_band = len(digestions_dict[enzs]["cuts"]) == 0
one_no_bands = no_enzs_band or no_enzyme_band
if ((enzyme,) in digestions_dict) and one_no_bands:
if no_enzyme_band:
digestions_dict[digestion] = digestions_dict[enzs]
digestions_dict[digestion]["same_as"] = enzs
elif no_enzs_band:
dig = (enzyme,)
digestions_dict[digestion] = digestions_dict[dig]
digestions_dict[digestion]["same_as"] = dig
else:
digestions_dict[digestion] = _merge_digestions(
digestion1=get_cuts(enzyme),
digestion2=digestions_dict[enzs],
sequence_length=len(sequence),
linear=linear,
)
digestions_dict[digestion]["same_as"] = digestion
digestions_dict.pop(())
# Reordering the dictionnary makes the computation of scores faster
# using 'same_as' to avoid recomputing scores involving similar patterns
digestions_dict = OrderedDict(
sorted(
digestions_dict.items(),
key=lambda item: (len(item[0]), len(item[1]["cuts"])),
)
)
return digestions_dict