def parse_motifs(raw_motifs, model_info, mod_set):
if mod_set is not None:
mod_set = set(mod_set)
can_bases = set()
for mod_base, can_base in model_info.mod_base_to_can.items():
if mod_set is not None and mod_base not in mod_set:
continue
can_bases.add(can_base)
if raw_motifs is None:
return [(mh.compile_motif_pat(can_base), 0) for can_base in can_bases]
motifs = []
for raw_motif, rel_pos in raw_motifs:
rel_pos = int(rel_pos)
if raw_motif[rel_pos] not in can_bases:
LOGGER.warning(
('Motif "{}" not associated with requested modified ' +
'bases.').format(raw_motif))
continue
motifs.append((mh.compile_motif_pat(raw_motif), rel_pos))
return motifs
def parse_motifs(raw_motifs):
motifs = []
for raw_motif, bases_before in raw_motifs:
bases_before = int(bases_before)
bases_after = len(raw_motif) - bases_before - 1
motif = mh.compile_motif_pat(raw_motif)
rc_motif = mh.compile_rev_comp_motif_pat(raw_motif)
motifs.append(
MOTIF_INFO(bases_before=bases_before,
bases_after=bases_after,
raw_motif=raw_motif,
motif=motif,
rc_motif=rc_motif))
return motifs