def test_moclo_compatible(self):
# alpha and omega vectors have recsites for this enzymes
feature = Feature.objects.get(uniquename='pDGB1_alpha1')
assert has_rec_sites(feature.residues, enzymes=('BpiI', 'BsaI'))
feature = Feature.objects.get(uniquename='pUPD')
assert has_rec_sites(feature.residues, enzymes=('BpiI', 'BsaI'))
feature = Feature.objects.get(uniquename='pAn11')
assert feature.moclo_compatible
feature = Feature.objects.get(uniquename='pDGB1_alpha1')
assert feature.moclo_compatible == 'not_evaluable'
f1 = Feature.objects.get(uniquename='pDelila')
assert not f1.moclo_compatible
def domestication_crispr(seq, category=None, prefix=None, suffix=None):
if len(seq) < 20:
raise ValueError('Seq length must be at least 20')
if len(seq) != 20 and category:
msg = 'To domesticate with the given target type, the CRISPR target '
msg += 'size must be 20'
raise ValueError(msg)
if category == TARGET_DICOT and str(seq[0]).upper() != 'G':
raise ValueError('First nucleotide must be G for target dicot category')
if category == TARGET_MONOCOT and str(seq[0]).upper() != 'A':
raise ValueError('First nucleotide must be G for target monocot category')
if has_rec_sites(seq):
msg = 'This secuence can not be domesticated. It has internal restriction sites'
raise ValueError(msg)
if category:
prefix = prefix[:3]
try:
count = Count.objects.get(name=CRYSPER_SEQ)
except Count.DoesNotExist:
count = Count.objects.create(name=CRYSPER_SEQ, value=1)
next_value = count.next
prepared_seq = Seq(prefix + seq + suffix)
seq_name = CRYSPER_SEQ + '_' + next_value
new_seq_record = SeqRecord(prepared_seq, name=seq_name, id=seq_name)
return new_seq_record
def moclo_compatible(self):
if not self.level or self.level != LEVEL_0 or self.type.name in (TARGET_DICOT, TARGET_MONOCOT):
return 'not_evaluable'
if self.vector.resistance not in (MOCLO_INCOMPATIBLE_RESISTANCES):
enzyme = self.enzyme_out[0]
residues = self.residues
pref_idx, suf_idx = get_prefix_and_suffix_index(residues, enzyme)[:2]
seq = residues[pref_idx:suf_idx + len(self.suffix)]
# TODO: maybe we should look only to the part seq. not with the vector
return not has_rec_sites(seq, enzymes=('BpiI', 'BsaI'))
else:
return False
def clean_seq(self):
seq = self.cleaned_data['seq']
category = self.cleaned_data.get('category', None)
if len(seq) < 20:
raise ValidationError('Seq length must be at least 20')
if len(seq) != 20 and category is not None:
msg = 'CRISPR target seq length must be 20 nucleotides'
raise ValidationError(msg)
if not _seq_is_dna(seq):
raise ValidationError('Seq must only contain ACTG')
if has_rec_sites(seq):
msg = 'This secuence can not be domesticated.'
msg += 'It has internal restriction sites'
raise ValidationError(msg)
return seq
