#!/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

module load QIIME2/2019.7

subject=( A J S An )
for x in "${subject[@]}"
do

tablein=/data/mramseylab/raw_reads/trip"$x"/paired-pseudo-denoise-table-"$x".qza
metadir=/data/mramseylab/metadata/plaque_meta_"$x".tsv
filtdir=/data/mramseylab/raw_reads/trip"$x"
visdir=/data/mramseylab/scripts/ALScripts/triptest/visualizations_"$x"
rawdir=/data/mramseylab/raw_reads/trip"$x"
fil=/filter

array=( basal BS SS SHI )
for i in "${array[@]}"
do
qiime feature-table filter-samples \
  --i-table $tablein \
  --m-metadata-file $metadir \
  --p-where "[media] = ('invivo','"$i"')" \
  --o-filtered-table $filtdir$fil/denoise-filtered-"$i".qza \

qiime feature-table summarize \
    --i-table $filtdir$fil/denoise-filtered-"$i".qza \
    --o-visualization $filtdir$fil/denoise-filtered-"$i".qzv \
    --m-sample-metadata-file $metadir \

done
done