#!/bin/bash -l
#SBATCH --job-name=AnnotateCazomeslargergroup
#SBATCH --time=24:00:00          # Max job time
#SBATCH -n 16                     # Number of cores requested
#SBATCH -N 1                     # Number of nodes requested
#SBATCH -p singlenode            # Job sharing between nodes
#SBATCH --mail-type=begin        # Send email when job begins
#SBATCH --mail-type=end          # Send email when job ends
#SBATCH --mail-type=fail         # Send email if job fails
#SBATCH --mail-user=pmb9@st-andrews.ac.uk

CUR_DATE=`date +%d_%m_%Y_%H_%M`

cd ~/Bioinformatics/CazomeMiningPipeline
conda activate dbcan_cazomevolve_3.9

cazomevolve get_cazy_cazymes \
    ~/Bioinformatics/CazomeMiningPipeline/data/reference/ncbi_genomes/22-02-2024 \
    ~/Bioinformatics/CazomeMiningPipeline/data/reference/local_cazy_dbs/06-07-2023/localcazydb060723.db \
    ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/cazomevolve_output/$CUR_DATE/notincazydb \
    ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/cazomevolve_output/$CUR_DATE/cazymesident/famgen.txt \
    ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/cazomevolve_output/$CUR_DATE/cazymesident/famgenacc.txt \
    -f -n

cazomevolve run_dbcan \
    ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/cazomevolve_output/$CUR_DATE/notincazydb \
    ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/dbcan_output/$CUR_DATE/output \
    4

cp -r ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/cazomevolve_output/$CUR_DATE/cazymesident ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/dbcan_output/$CUR_DATE

cazomevolve get_dbcan_cazymes \
    ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/dbcan_output/$CUR_DATE/output \
    ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/cazomevolve_output/$CUR_DATE/cazymesident/famgen.txt \
    ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/cazomevolve_output/$CUR_DATE/cazymesident/famgenacc.txt \
    -f -n

cazomevolve add_taxs pmb9@st-andrews.ac.uk \
    --FG_FILE ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/cazomevolve_output/$CUR_DATE/cazymesident/famgen.txt \
    --FGP_FILE ~/Bioinformatics/CazomeMiningPipeline/data/cleaned/cazomevolve_output/$CUR_DATE/cazymesident/famgenacc.txt \
    --tax_family \
    --genus \
    --species