#!/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/proc_reads/taxon-filtered/taxon-filtered-table.qza
metadir=/data/mramseylab/metadata/plaque_meta_3.tsv
filtdir=/data/mramseylab/proc_reads/
fil=Master-Filtered

mkdir $filtdir$fil

qiime feature-table filter-samples \
  --i-table $tablein \
  --m-metadata-file $metadir \
  --p-where "[PACT]='N'" \
  --o-filtered-table  $filtdir$fil/table-master-filtered.qza

  done

qiime taxa barplot \
  --i-table $tablein2 \
  --i-taxonomy $clsdir \
  --m-metadata-file $metadir \
  --o-visualization $filtdir$fil/taxon-filtered-table-barplot.qzv

  #use this to see if filtering worked

#Generate viewable feature table to look for ASVs of interest / filtering stats
qiime feature-table summarize \
  --i-table $filtdir$fil/taxon-filtered-table.qza \
  --o-visualization $filtdir$fil/taxon-table-for-looking.qzv \
  --m-sample-metadata-file $metadir