def add_sequence(gi, variant_model, taxonomy, header, sequence):
if not variant_model.core_type.id == "H1" and not variant_model.core_type.id == "Unknown":
hist_identified, ss_position, sequence = get_hist_ss(sequence, variant_model.core_type.id, save_alignment=True)
sequence = str(sequence.seq)
else:
ss_position = defaultdict(lambda: (None, None))
sequence = str(sequence)
seq = Sequence(
id = gi,
variant = variant_model,
gene = None,
splice = None,
taxonomy = taxonomy,
header = header,
sequence = sequence,
reviewed = False,
)
seq.save()
return seq
def update_features(seq, ss_position=None, variant_model=None, return_not_save=False):
if ss_position is None and variant_model is not None:
hist_identified, ss_position, sequence = get_hist_ss(seq.to_biopython(ungap=True).seq, variant_model.core_type.id, save_alignment=True)
sequence = str(sequence.seq)
if ss_position is None:
assert 0
if hasattr(seq, "features") and seq.features:
seq.features.delete()
if not variant_model.core_type.id == "H1":
features = Features.from_dict(seq, ss_position)
if return_not_save:
return features
try:
features.save()
except:
pass