def assemble_parts(parts, part_types):
'We build the parts using the form data'
part_types.append(VECTOR_TYPE_NAME)
joined_seq = SeqRecord(Seq('', alphabet=generic_dna))
names = {'parts': []}
for part_type in part_types:
part_uniquename = parts[part_type]
part = Feature.objects.get(uniquename=part_uniquename)
gb_path = os.path.join(proj_settings.MEDIA_ROOT,
part.genbank_file.name)
part_record = SeqIO.read(gb_path, 'gb')
seq = Seq(part.residues)
# crispr targets are the unique parts that are not vectors
# and does not have a verctor
if part.vector is None and part.type.name != VECTOR_TYPE_NAME:
pref_idx = 0
suf_idx = len(seq) - len(part.suffix)
names['parts'].append(part.uniquename)
else:
if part.type.name == VECTOR_TYPE_NAME:
enzyme = part.enzyme_in[0]
names['vector'] = part.uniquename
else:
names['parts'].append(part.uniquename)
enzyme = part.enzyme_out[0]
pref_idx, suf_idx = get_prefix_and_suffix_index(seq, enzyme)[:2]
# VECTOR must be always the last part to add
if part.type.name == VECTOR_TYPE_NAME and part.direction == REVERSE:
if suf_idx >= pref_idx and suf_idx + 4 < len(seq):
part_sub_seq = part_record[pref_idx + 4:suf_idx + 4]
else:
part_sub_seq = part_record[pref_idx + 4:]
part_sub_seq += part_record[:suf_idx + 4]
joined_seq = joined_seq.reverse_complement() + part_sub_seq
else:
if suf_idx >= pref_idx:
part_sub_seq = part_record[pref_idx:suf_idx]
else:
part_sub_seq = part_record[pref_idx:]
part_sub_seq += part_record[:suf_idx]
joined_seq += part_sub_seq
try:
count = Count.objects.get(name=ASSEMBLED_SEQ)
except Count.DoesNotExist:
count = Count.objects.create(name=ASSEMBLED_SEQ, value=1)
next_value = count.next
joined_seq.id = ASSEMBLED_SEQ + '_' + next_value
joined_seq.name = joined_seq.id
joined_seq.description = "({0}){1}".format(','.join(names['parts']),
names['vector'])
return joined_seq
def get_prefix_and_suffix(seq, enzyme):
'it gets the prefix and the suffix of the feature seq'
try:
result = get_prefix_and_suffix_index(seq, enzyme)
prefix_index, suffix_index, prefix_size = result
except RuntimeError as error:
if str(error) == "No rec_site":
return None, None
else:
raise
return _get_pref_suff_from_index(seq, prefix_index, suffix_index,
prefix_size)
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 _get_stripped_vector_seq():
pupd = Feature.objects.get(uniquename=DOMESTICATED_VECTOR)
vec_seq = pupd.residues
pre_suf_size = get_prefix_and_suffix_index(vec_seq, pupd.enzyme_in[0])
prefix_index, suffix_index, prefix_size = pre_suf_size
prefix_start = prefix_index
suffix_end = suffix_index + prefix_size
if prefix_start > suffix_end:
stripped_seq = vec_seq[prefix_start:]
stripped_seq += vec_seq[:suffix_end]
else:
stripped_seq = vec_seq[prefix_start:suffix_end]
return stripped_seq
