def _get_restr_type(name):
'''Gets RestrictionType from name.'''
types = [
x for _, (x, y) in Restriction_Dictionary.typedict.items() if name in y
][0]
enz_types = tuple(getattr(Restriction, typ) for typ in types)
return Restriction.RestrictionType(str(name), enz_types,
Restriction_Dictionary.rest_dict[name])
def get_enzyme_instance_ipython(enz_name):
"""
An alternative method to fetch an instance of a given restriction enzyme by its
name using a work-around which avoids exception with getattr() in iPython.
Ackn: StackOverflow: user xbello.
See: http://stackoverflow.com/questions/20381912/type-object-restrictiontype-has-no-attribute-size
:param enz_name: the case-sensitive name of the enzyme
:return: RestrictionType the enzyme instance
"""
r_type_names = [rt for tid, (rt, rn) in typedict.iteritems() if enz_name in rn][0]
r_clz = tuple(getattr(Restriction, rt) for rt in r_type_names)
return Restriction.AbstractCut(enz_name, r_clz, rest_dict[enz_name])
def censor_record(
record,
record_id="censored",
label_generator="feature_%d",
keep_topology=False,
anonymise_features=True,
preserve_sites=None,
):
"""Return a record with random sequence and censored annotations/features.
Useful for creating example files or anonymising sequences for bug reports.
Parameters
----------
record
The record to be anonymized.
record_id
ID of the new record.
label_generator
Recipe to change feature labels. Either ``"feature_%d"`` or ``None`` (no label)
of a function (i, feature)=>label.
keep_topology
Whether to keep the record topology or not.
anonymise_features
Whether to replace feature labels and ID/name, or not.
preserve_sites
List of enzyme sites to keep. Example: ``["BsmBI", "BsaI"]``. Preserves the
sequence around cut sites of the specified enzymes.
"""
# Anonymise
if anonymise_features:
new_record = anonymized_record(
record, record_id=record_id, label_generator=label_generator
)
else:
new_record = deepcopy(record)
if keep_topology:
try:
new_record.annotations["topology"] = record.annotations["topology"]
except KeyError: # input may not have topology set
pass
# Randomise
new_seq = random_dna_sequence(
len(new_record), gc_share=None, probas=None, seed=None
)
if preserve_sites:
restriction_batch = Restriction.RestrictionBatch(preserve_sites)
# Destroy random new enzyme sites:
analysis = Restriction.Analysis(restriction_batch, sequence=Seq(new_seq))
analysis_results = analysis.full()
for enzyme, hits in analysis_results.items():
for hit in hits:
# 10 bp up- and downstream destroys the site whichever strand it is on:
if hit - 10 < 0: # handle edge cases
start = 0
upstream = "A" * hit
else:
start = hit - 10
upstream = "A" * 10
if hit + 10 > len(new_seq):
end = len(new_seq)
downstream = "A" * (len(new_seq) - hit)
else:
end = hit + 10
downstream = "A" * 10
replacement = upstream + downstream
new_seq = easy_dna.replace_segment(new_seq, start, end, replacement)
# Add original sites:
analysis = Restriction.Analysis(restriction_batch, sequence=record.seq)
analysis_results = analysis.full()
original_seq = str(record.seq)
for enzyme, hits in analysis_results.items():
for hit in hits:
# keep 12 bp surrounding the cut site, to capture enzyme site:
if hit - 12 < 0: # handle edge cases
start = 0
else:
start = hit - 12
if hit + 12 > len(new_seq):
end = len(new_seq)
else:
end = hit + 12
original_segment = original_seq[start:end]
new_seq = easy_dna.replace_segment(
new_seq, start, end, original_segment
)
censored_record = record_with_different_sequence(new_record, new_seq)
return censored_record
def test_init(self):
"""Check for error during __init__."""
with self.assertRaises(ValueError) as ve:
Restriction.OneCut('bla-me', (Restriction.RestrictionType, ),
dict())
self.assertIn('hyphen', str(ve.exception))
def createAnalysis(self, seq_str, batch_ary):
"""Restriction.Analysis creation helper method."""
rb = Restriction.RestrictionBatch(batch_ary)
seq = Seq(seq_str)
return Restriction.Analysis(rb, seq)
def test_init(self):
"""Check for error during __init__."""
with self.assertRaises(ValueError) as ve:
Restriction.OneCut("bla-me", (Restriction.RestrictionType, ), {})
self.assertIn("hyphen", str(ve.exception))