def centroid_homfold_fast_prep(all_seqs, query, n, len_diff):
ml.debug(fname())
assert n >= 1, "Number of sequences for centroid-fast must be greater then 0."
if query.annotations['ambiguous']:
msgfail = "Query sequence contains ambiguous characters. Can't use centroid-fast."
ml.error(msgfail)
raise AmbiguousQuerySequenceException(msgfail)
nr_na_ld = BA_support.sel_seq_simple(all_seqs, query, len_diff)
nr_na_ld_n = nr_na_ld[:int(n)]
return nr_na_ld_n
def turbofold_fast(all_seqs, seqs2predict, query, cpu, n, turbofold_params,
len_diff, pkey, sha1val):
"""Run Turbo-fast prediction
- ambiguous sequences cannot be predicted with TurboFold
- do not predict sequence twice
- seqs2predict must be subset of all_seqs
"""
ml.debug(fname())
# this is backup (in rboAnalyzer this is handled on higher level)
if query.annotations['ambiguous']:
msgfail = "Query sequence contains ambiguous characters. Can't use Turbo-fast."
ml.error(msgfail)
raise exceptions.AmbiguousQuerySequenceException(msgfail)
nr_na_ld = BA_support.sel_seq_simple(all_seqs, query, len_diff)
return turbofold_ext_nr_fast(seqs2predict, nr_na_ld, cpu, n,
turbofold_params, pkey, sha1val)