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Replace ignore positions with ASCII symbol
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padix-key committed Sep 13, 2024
1 parent d0107fa commit 91c866b
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions doc/examples/scripts/sequence/homology/genome_comparison.py
Original file line number Diff line number Diff line change
Expand Up @@ -67,15 +67,15 @@
# 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()]

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()],
)

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