# micromamba activate buisciii-tools_2.1.0

mkdir logs
mkdir assemblies
mkdir MLVA_output
scratch_dir=$(pwd | sed 's|/data/ucct/bi/scratch_tmp|/scratch|g')
cp ../../*_ASSEMBLY/03-assembly/unicycler/*.fasta* assemblies/
gzip -d assemblies/*.fasta.gz
available_primers=$(ls /data/ucct/bi/references/MLVA/*primer* | rev | cut -d "/" -f1 | rev | cut -d "_" -f1)

echo "Available primers:"
select primer in $available_primers; do
    if [ -n "$primer" ]; then
        echo "You selected: $primer"
        break
    else
        echo "Invalid selection. Please try again."
    fi
done

primer_file=$(ls /data/ucct/bi/references/MLVA/${primer}*)

echo "srun --partition short_idx --chdir ${scratch_dir} --output logs/MLVA.log --job-name MLVA python /data/ucct/bi/pipelines/mlva/MLVA_finder.py -c -i assemblies -o MLVA_output -p ${primer_file} --full-locus-name --predicted-PCR-size-table --flanking-seq 20 &"  > _01_mlva.sh
