#!/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

tablein=/data/mramseylab/raw_reads/2023_SUPP_V1V2/master-denoise-table-v1v2-paired.qza
metadir=/data/mramseylab/metadata/plaque_meta_6.tsv
filtdir=/data/mramseylab/proc_reads/2023_Master
rawdir=/data/mramseylab/raw_reads/2023_SUPP_V1V2
fil=/FilteredSamples

mkdir $filtdir$fil

array=( subjectA subjectAn subjectJ subjectS )

for i in "${array[@]}"
do
qiime feature-table filter-samples \
  --i-table $tablein \
  --m-metadata-file $metadir \
  --p-where "[subject] = ('$i')" \
  --o-filtered-table  $filtdir/master-denoise-table_$i.qza

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

qiime feature-table filter-features \
      --i-table $filtdir/master-denoise-table_$i.qza \
      --p-min-frequency 5 \
      --o-filtered-table $filtdir$fil/master-denoise-filtered-5_$i.qza

    #Making visualization at each step to monitor loss of taxa numbers
    qiime feature-table summarize \
      --i-table $filtdir$fil/master-denoise-filtered-5_$i.qza \
      --o-visualization $filtdir$fil/filter_feq_5_$i.qzv \
      --m-sample-metadata-file $metadir \

    qiime feature-table filter-features \
      --i-table $filtdir$fil/master-denoise-filtered-5_$i.qza \
      --p-min-samples 2 \
      --o-filtered-table $filtdir$fil/filter_feat_2_feq_5_$i.qza

    qiime feature-table summarize \
      --i-table $filtdir$fil/filter_feat_2_feq_5_$i.qza \
      --o-visualization $filtdir$fil/filter_feat_2_feq_5_$i.qzv \
      --m-sample-metadata-file $metadir \

    done