def generate_consensus(session, clone_ids):
"""Generates consensus CDR3s for clones.
:param Session session: The database session
:param list clone_ids: The list of clone IDs to assign to groups
"""
if len(clone_ids) == 0:
return
for clone in funcs.periodic_commit(
session,
session.query(Clone).filter(Clone.id.in_(clone_ids)),
interval=1000):
seqs = session.query(
Sequence
).join(SequenceCollapse).filter(
Sequence.clone_id == clone.id,
SequenceCollapse.copy_number_in_subject > 0
).all()
clone.cdr3_nt = funcs.consensus([s.cdr3_nt for s in seqs])
clone.cdr3_aa = lookups.aas_from_nts(clone.cdr3_nt)
clone.germline = generate_germline(session, seqs, clone)
session.commit()
def generate_consensus(session, clone_ids):
"""Generates consensus CDR3s for clones.
:param Session session: The database session
:param list clone_ids: The list of clone IDs to assign to groups
"""
if not clone_ids:
return
for clone in funcs.periodic_commit(session,
session.query(Clone).filter(
Clone.id.in_(clone_ids)),
interval=1000):
seqs = session.query(Sequence).join(SequenceCollapse).filter(
Sequence.clone_id == clone.id,
SequenceCollapse.copy_number_in_subject > 0).all()
clone.cdr3_nt = funcs.consensus([s.cdr3_nt for s in seqs])
clone.cdr3_aa = lookups.aas_from_nts(clone.cdr3_nt)
clone.germline = generate_germline(session, seqs, clone)
clone.overall_total_cnt = sum([s.copy_number for s in seqs])
clone.functional = (clone.cdr3_num_nts % 3 == 0
and '*' not in clone.cdr3_aa
and not lookups.has_stop(clone.germline))
session.commit()
def get_ties(self, genes):
length = len(self[genes[0]])
key = tuple(sorted(genes))
if key in self.ties:
return self.ties[key]
step = 1 if self.gene == 'v' else -1
seqs = [self[v].ljust(length, 'N')[::step] for v in genes]
cons = funcs.consensus(seqs)[::step]
return self.ties.setdefault(key, cons)