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 generate_germline(session, seqs, clone):
rep_seq = seqs[0]
cdr3_start_pos = sum(rep_seq.regions[:5])
germline = rep_seq.germline[:cdr3_start_pos]
germline += '-' * clone.cdr3_num_nts
clone.functional = (len(germline) % 3 == 0
and not lookups.has_stop(germline))
j_region = rep_seq.germline[cdr3_start_pos + rep_seq.cdr3_num_nts:]
germline += j_region
return germline
def generate_germline(session, seqs, clone):
rep_seq = seqs[0]
cdr3_start_pos = sum(rep_seq.regions[:5])
germline = rep_seq.germline[:cdr3_start_pos]
germline += '-' * clone.cdr3_num_nts
clone.functional = (
len(germline) % 3 == 0 and
not lookups.has_stop(germline)
)
j_region = rep_seq.germline[cdr3_start_pos + rep_seq.cdr3_num_nts:]
germline += j_region
return germline
def stop(self):
return lookups.has_stop(self.sequence)
def stop(self):
return lookups.has_stop(self.sequence)