#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=48g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

array=( An )

for i in "${array[@]}"
do
tablein=/data/mramseylab/raw_reads/trip"$i"/paired-pseudo-denoise-table-"$i".qza
metadir=/data/mramseylab/metadata/plaque_meta_"$i".tsv
filtdir=/data/mramseylab/raw_reads/trip"$i"
visdir=/data/mramseylab/scripts/ALScripts/triptest/visualizations_"$i"
rawdir=/data/mramseylab/raw_reads/trip"$i"
fil=/filter

mkdir $filtdir$fil


qiime feature-table filter-features \
      --i-table $tablein \
      --p-min-frequency 5 \
      --o-filtered-table $filtdir$fil/5-denoise-pseudo-paired-"$i".qza

    #Making visualization at each step to monitor loss of taxa numbers
    qiime feature-table summarize \
      --i-table $filtdir$fil/5-denoise-pseudo-paired-"$i".qza \
      --o-visualization $filtdir$fil/filter_feq_5-"$i".qzv \
      --m-sample-metadata-file $metadir \

    #filter for features present in more than 2 libraries
    qiime feature-table filter-features \
      --i-table $filtdir$fil/5-denoise-pseudo-paired-"$i".qza \
      --p-min-samples 2 \
      --o-filtered-table $filtdir$fil/denoise-pseudo_feat_2_feq_5-"$i".qza

    qiime feature-table summarize \
      --i-table $filtdir$fil/denoise-pseudo_feat_2_feq_5-"$i".qza\
      --o-visualization $filtdir$fil/denoise-pseudo_feat_2_feq_5-"$i".qzv \
      --m-sample-metadata-file $metadir \

done