#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

# this script is a way to make the data more uniform, you must look the summary table made to
# figure out what numbers you need depending on what youre doing

module load QIIME2/2024.2


rawdir=/data/mramseylab/raw_reads/2023_AL_SUPP/triplicates/tripS
metadir=/data/mramseylab/16S/metadata/plaque_meta_S.tsv
visdir=/data/mramseylab/16S/visualizations/AL_2023

if qiime feature-table filter-samples \
  --i-table $rawdir/paired-pseudo-denoise-table-S.qza \
  --m-metadata-file $metadir \
  --p-where "[media]='basal' OR [media]='invivo' " \
  --o-filtered-table $rawdir/S-saliva-table.qza; then
echo "subject filtered"
fi 

if qiime diversity alpha-rarefaction \
  --i-table $rawdir/S-saliva-table.qza \
  --i-phylogeny $rawdir/rooted-tree-pseudo-S.qza \
  --p-max-depth 6000 \
  --m-metadata-file $metadir \
  --o-visualization $visdir/alpha-rarefaction-subject-S-6000-2023.qzv; then 
echo "visual made"
fi