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

module load QIIME2/2019.7

tablein=/data/mramseylab/proc_reads/SF-hum/SF-hum-table.qza
clsdir=/data/mramseylab/classifiers/
metadir=/data/mramseylab/metadata/
visdir=/data/mramseylab/visualizations/
filtdir=/data/mramseylab/proc_reads/

# filter status of input files, "ctrl-filter" is just for taxa belonging to no template controls
fil=NP-hum
#must make the directory you are filtering to 1st or else it will error
mkdir $filtdir$fil

#Filtering list from mock samples was generated previously with the strict-filter.sh script

qiime taxa filter-table \
  --i-table $tablein \
  --i-taxonomy $clsdir\silva-mod-taxonomy2.qza \
  --p-mode contains \
  --p-exclude "Pseudomonas" \
  --o-filtered-table $filtdir$fil/$fil-table.qza

#Use excluded table to generate barplot for checking
qiime taxa barplot \
  --i-table $filtdir$fil/$fil-table.qza \
  --i-taxonomy $clsdir\silva-mod-taxonomy2.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --o-visualization $filtdir$fil/$fil-table-barplot.qzv

#Generate viewable feature table to look for ASVs of interest / filtering stats
qiime feature-table summarize \
  --i-table $filtdir$fil/$fil-table.qza \
  --o-visualization $filtdir$fil/$fil-table.qzv \
  --m-sample-metadata-file $metadir\Serum5.tsv