From 91c866b856e56923a90c45d19237bb60239f2d41 Mon Sep 17 00:00:00 2001 From: Patrick Kunzmann Date: Fri, 13 Sep 2024 10:19:13 +0200 Subject: [PATCH] Replace ignore positions with ASCII symbol --- doc/examples/scripts/sequence/homology/genome_comparison.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/examples/scripts/sequence/homology/genome_comparison.py b/doc/examples/scripts/sequence/homology/genome_comparison.py index 066388ce5..52802ee0f 100644 --- a/doc/examples/scripts/sequence/homology/genome_comparison.py +++ b/doc/examples/scripts/sequence/homology/genome_comparison.py @@ -67,7 +67,7 @@ # Second, spaced *k-mers* :footcite:`Ma2002` are used instead of # continuous ones to increase the sensitivity. # However, not every spacing model performs equally well, so the proven -# one ``111∗1∗11∗1∗∗11∗111`` :footcite:`Choi2004` is used here. +# one ``111*1*11*1*11*111`` :footcite:`Choi2004` is used here. repeat_mask = tantan.TantanApp.mask_repeats(bacterium_seq) bacterium_seqs = [bacterium_seq, bacterium_seq.reverse(copy=False).complement()] @@ -75,7 +75,7 @@ table = align.KmerTable.from_sequences( k=12, sequences=bacterium_seqs, - spacing="111∗1∗11∗1∗∗11∗111", + spacing="111*1*11*1*11*111", ignore_masks=[repeat_mask, repeat_mask[::-1].copy()], )