Open chrisgulvik opened 1 year ago
This is a hackish workaround to accomplish it for type strains for the time being.
git clone git@github.com:lmc297/BTyper3.git
mkdir -p Btyper3/seq_ani_db/typestrains
awk '{print $1 "\t" $3}' \
Btyper3/seq_ani_db/typestrains/typestrains.tsv \
> BTyper3/archive/scripts/seq_ani_db/typestrains/typestrains.txt
sed -i '1 s/./#&/' BTyper3/archive/scripts/seq_ani_db/typestrains/typestrains.txt
cd Btyper3/archive/scripts
./build_btyper3_ani_db.py -db typestrains-only
for f in *.gz.gz; do
[ -f "$f" ] && mv -v "$f" "${f%.gz.gz}.gz"
done
ls B_*.fna.gz | wc -l
# RESULTS: n=29 files
The data files are installed with the rest of the Python code, so you should can find the path with the following command:
$ python -c 'import btyper3; print(btyper3.__path__[0])'
/home/althonos/.local/lib/python3.11/site-packages/btyper3
To enable further follow-up work on the exact files used for comparison, for example for the genomes using ANI, could a feature be added to specify an outpath where the files are stored?