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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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mask_gubbins_aln.py #321

Closed xuechunxu closed 12 months ago

xuechunxu commented 2 years ago

Hi，

When I used mask_gubbins_aln.py to mask recombination regions: python ~/.conda/envs/gubbins-env/bin/mask_gubbins_aln.py --aln clean.full.aln --gff gubbins.recombination_predictions.gff --out clean.full.masked.aln It called an error: ~/.conda/envs/gubbins-env/lib/python3.9/site-packages/Bio/Seq.py:1754: BiopythonDeprecationWarning: myseq.tomutable() is deprecated; please use MutableSeq(myseq) instead. warnings.warn(

amymariecampbell commented 2 years ago

I'm getting this error too- did you find any solutions?

nickjcroucher commented 2 years ago

This is just a warning, the output should be fine unless there is another error - we will update this code soon.

amymariecampbell commented 2 years ago

Great- thank you!