DTR removing about cenote-taker2

[mtisza1]

Alberto,

Thanks for reaching out. Yes, this was a bug I found that effected v2.1.2 and probably a few earlier versions. I fixed this for v2.1.5, and added the --wrap option. When you pass --wrap True (default option), the DTR will be clipped and the sequence will be rotated. When you pass --wrap False, the sequence will not be clipped or rotated, but the DTR sequences will be reported as a feature in the .gbf file. It looks like I forgot to report the bug fix in the release notes.

Relatedly, you can pass --exact_dtrs True to require that the 5' and 3' DTR sequence matches exactly (the default mode is based on bitscore of the alignment.

To update to v2.1.5:

conda activate cenote-taker2_env
pip install phanotate
conda install -c conda-forge -c bioconda hhsuite last=1282 seqkit

### you may have to use conda to install biopython and bedtools as well ###

cd Cenote-Taker2
git pull

python update_ct2_databases.py --hmm True --protein True

I hope this was helpful for you!

Best,

Mike