From f09cd39ece6ddc782cdb4e3f56acdbe35e8d4b37 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 25 Sep 2024 09:00:57 -0400 Subject: [PATCH] refact(call): move motif-size k-mer calc iter to function --- strkit/call/call_locus.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/strkit/call/call_locus.py b/strkit/call/call_locus.py index 9c31636..8302c20 100644 --- a/strkit/call/call_locus.py +++ b/strkit/call/call_locus.py @@ -782,6 +782,11 @@ def debug_log_flanking_seq(logger_: logging.Logger, locus_log_str: str, rn: str, ) +def _calc_motif_size_kmers(tr_read_seq_wc: str, tr_len: int, motif_size: int): + for i in range(tr_len - motif_size + 1): + yield tr_read_seq_wc[i:i + motif_size] + + def _ndarray_serialize(x: Iterable) -> list[Union[int, np.int_]]: return list(map(round, x)) @@ -1159,7 +1164,7 @@ def get_read_length_partition_mean(p_idx: int) -> float: if count_kmers != "none": read_kmers.clear() - read_kmers.update(tr_read_seq_wc[i:i+motif_size] for i in range(0, tr_len - motif_size + 1)) + read_kmers.update(_calc_motif_size_kmers(tr_read_seq_wc, tr_len, motif_size)) rc_timer = time.perf_counter() # Set initial integer copy number guess based on aligned TR size, plus the previous read offset (how much the