INNER CODE UNIT · Python
js
antigenomics/vdjtools · python/vdjtools/cli/__init__.py:182
js = df[j_col].to_list() if j_col and j_col in df.columns else [None] * len(seqs)
# One batched native call per kind, never one call per sequence: both batch entry points
# release the GIL and thread across the input. Detection is per sequence, so the two kinds are
# interleaved -- split by index, score each group, scatter back into input order.
pg: list[float] = [0.0] * len(seqs)
groups: dict[bool, list[int]] = {True: [], False: []}
for i, s in enumerate(seqs):
if s:
groups[_is_nt(s) if seq_type == "auto" else (seq_type == "nt")].append(i)
for is_nt, idx in groups.items():
if not idx:
continue
sub, subv, subj = [seqs[i] for i in idx], [vs[i] for i in idx], [js[i] for i in idx]
got = (native.pgen_nt_batch(m, sub, subv, subj) if is_nt else
native.pgen_aa_batch(m, sub, subv, subj, mismatches=mismatches))
for i, p in zip(idx, got):
pg[i] = p